1887

Abstract

A novel actinomycete, designated strain S6R2A4-9, was isolated from a soil sample collected from a karst cave in Henan Province, China, and subjected to a polyphasic taxonomic study. This isolate grew optimally at 25–28 °C, pH 6.5–8.0 and in the absence of NaCl. The substrate mycelium of the isolate was well developed with irregular branches. Aerial mycelium fragmented into long, rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S6R2A4-9 resided in the cluster of the genus within the family and shared the highest 16S rRNA gene sequence similarity (98.98 %) with I12A-02601. The G+C content of the genomic DNA was 67.0 mol%. The strain contained glucose, ribose and xylose in its whole-cell hydrolysates. Strain S6R2A4-9 possessed a novel variation of peptidoglycan derived from the type A1γ -Dpm-direct. The polar lipids consisted of diphosphatidylglycerol, -acetylglucosamine-containing phospholipid, phosphatidylinositol mannoside, phosphatidylglycerol, phosphoglycolipids and glycolipids. The predominant menaquinones were MK-10(H) and MK-10(H). The major fatty acids were C, iso-C and 10-methyl C. The level of DNA–DNA relatedness between strain S6R2A4-9 and I12A-02601 was 27.6 ± 3.0 %, which was low enough to indicate that the strain represents a distinct species of the genus . On the basis of the polyphasic taxonomic evidence, a novel species, sp. nov., is proposed. The type strain of the novel species is S6R2A4-9 ( = DSM 28944 = CGMCC 4.7241).

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2016-03-01
2024-03-28
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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 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 MediaEdited by Parks L. C. Boca Raton, FL: CRC Press;
    [Google Scholar]
  3. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230 [View Article][PubMed]
    [Google Scholar]
  4. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [View Article][PubMed]
    [Google Scholar]
  5. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  6. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  7. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
    [Google Scholar]
  8. Guo L., Tuo L., Habden X., Zhang Y., Liu J., Jiang Z., Liu S., Dilbar T., Sun C. 2015; Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 65:206–213 [View Article][PubMed]
    [Google Scholar]
  9. Hall T. A. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Window 95/98/NT. Nucleic Acids Symp Ser 41:95–98
    [Google Scholar]
  10. Hasegawa T., Takizawa M., Tanida S. 1983; A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322 [View Article]
    [Google Scholar]
  11. Kaewkla O., Franco C. M. M. 2011; Flindersiella endophytica gen. nov., sp. nov., an endophytic actinobacterium isolated from the root of Grey Box, an endemic eucalyptus tree. Int J Syst Evol Microbiol 61:2135–2140 [View Article][PubMed]
    [Google Scholar]
  12. Kelly K. L. 1964 Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office;
    [Google Scholar]
  13. 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]
  14. 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]
  15. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [View Article]
    [Google Scholar]
  16. Lee L.-H., Zainal N., Azman A.-S., Mutalib N.-S.A., Hong K., Chan K.-G. 2014; Mumia flava gen. nov., sp. nov., an actinobacterium of the family Nocardioidaceae . Int J Syst Evol Microbiol 64:1461–1467 [View Article][PubMed]
    [Google Scholar]
  17. Li W.-J., Xu P., Schumann P., Zhang Y.-Q., Pukall R., Xu L.-H., Stackebrandt E., Jiang C.-L. 2007; Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 57:1424–1428 [View Article][PubMed]
    [Google Scholar]
  18. Liu J.-M., Tuo L., Habden X., Guo L., Jiang Z.-K., Liu X.-F., Chen L., Zhang Y.-Q., Sun C.-H. 2015; Nesterenkonia populi sp. nov., an actinobacterium isolated from Populus euphratica . Int J Syst Evol Microbiol 65:1474–1479 [View Article][PubMed]
    [Google Scholar]
  19. Magee C. M., Rodeheaver G., Edgerton M. T., Edlich R. F. 1975; A more reliable gram staining technic for diagnosis of surgical infections. Am J Surg 130:341–346 [View Article][PubMed]
    [Google Scholar]
  20. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218 [View Article]
    [Google Scholar]
  21. Marmur J., Doty P. 1962; Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118 [View Article][PubMed]
    [Google Scholar]
  22. 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]
  23. 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]
  24. Miyoshi T., Iwatsuki T., Naganuma T. 2005; Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters. Appl Environ Microbiol 71:1084–1088 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. Prauser H. 1976; Nocardioides, a new genus of the order Actinomycetales . Int J Syst Bacteriol 26:58–65 [View Article]
    [Google Scholar]
  27. 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]
  28. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  29. Schumann P. 2011; Peptidoglycan structure. Methods Microbiol 38:101–129 [View Article]
    [Google Scholar]
  30. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [View Article]
    [Google Scholar]
  31. Sohn K., Hong S. G., Bae K. S., Chun J. 2003; Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov. Int J Syst Evol Microbiol 53:1005–1007 [View Article][PubMed]
    [Google Scholar]
  32. Sun H.-M., Zhang T., Wei Y.-Z., Liu H.-Y., Yu L.-Y., Zhang Y.-Q. 2015; Tenggerimyces mesophilus gen. nov., sp. nov., a member of the family Nocardioidaceae . Int J Syst Evol Microbiol 65:3359–3364 [View Article][PubMed]
    [Google Scholar]
  33. 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 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  34. 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]
  35. Waksman S. A. 1961 The Actinomycetes. Classification, Identification and Descriptions of Genera and Species vol. 2 Baltimore, MD: Williams & Wilkins;
    [Google Scholar]
  36. 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 [View Article][PubMed]
    [Google Scholar]
  37. Wayne L., Brenner D., Colwell 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 [View Article]
    [Google Scholar]
  38. Williams S. T., Goodfellow M., Alderson G., Wellington E. M. H., Sneath P. H. A., Sackin M. J. 1983; Numerical classification of Streptomycesand related genera. J Gen Microbiol 129:1743–1813[PubMed]
    [Google Scholar]
  39. Xu P., Li W.-J., Tang S.-K., Zhang Y.-Q., Chen G.-Z., Chen H.-H., Xu L.-H., Jiang C.-L. 2005; Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153 [View Article][PubMed]
    [Google Scholar]
  40. Yabe S., Aiba Y., Sakai Y., Hazaka M., Yokota A. 2011; Thermasporomyces composti gen. nov., sp. nov., a thermophilic actinomycete isolated from compost. Int J Syst Evol Microbiol 61:86–90 [View Article][PubMed]
    [Google Scholar]
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