1887

Abstract

A novel endophytic actinobacterium, designated strain CPCC 204076, was isolated from surface-sterilized tissue of the medicinal plant (Thunb.) collected from Sichuan Province, south-west China. The taxonomic position of the isolate was investigated by a polyphasic approach. The strainwas aerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped. Growth was observed at 10–37 °C, at pH 5.0–10.0 and with 0–3.0 % (w/v) NaCl. The polar lipid fraction consisted of diphosphatidylglycerol, a phospholipid, an aminolipid, a glycolipid, an aminophospholipid and phosphatidylinositol. The cell wall contained -diaminopimelic acid as the diagnostic diamino acid and the peptidoglycan was of type A4γ. The menaquinone system consisted of MK-9(H) and MK-8(H). The major cellular fatty acids (>10 %) were iso-C and anteiso-C. The genomic DNA G+C content of strain CPCC 204076 was found to be 71.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that CPCC 204076 belongs to the genus with highest sequence similarity to DSM 45627 (96.5 %), DSM 45908 (96.5 %) and JCM 30448 (96.1 %), and much lower similarities (<95.0 %) to other available 16S rRNA gene sequences from validly described pure cultures. However, DNA–DNA hybridyzation values between strain CPCC 204076 and the three recognized species were 31±3.1 % ( DSM 45627), 33±2.9 % ( DSM 45908) and 37±1.7 % ( JCM 30448), which were all far below the recommended cut-off value of 70 %. The phenotypic and genomic characteristics distinctly indicated that strain CPCC 204076 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CPCC 204076 (I13A-01604) (=DSM 46866=NBRC 110718).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001296
2016-10-01
2020-04-01
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/10/3972.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001296&mimeType=html&fmt=ahah

References

  1. Brunchorst J.. 1886; Über einige Wurzelanschwellungen besonders diejenigen von Alnus und den Elaeagnaceen. Bot Inst Tubingen2:151–177 (in German)
    [Google Scholar]
  2. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E.. 1977; Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  3. Compant S., Reiter B., Sessitsch A., Nowak J., Clément C., Ait Barka E.. 2005; Endophytic colonization of vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN. Appl Environ Microbiol71:1685–1693 [CrossRef][PubMed]
    [Google Scholar]
  4. De Ley J., Cattoir H., Reynaerts A.. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem12:133–143 [CrossRef][PubMed]
    [Google Scholar]
  5. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  6. Felsenstein J.. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution39:783–791 [CrossRef]
    [Google Scholar]
  7. Frank H., Rettenmeier A., Weicker H., Nicholson G. J., Bayer E.. 1980; A new gas chromatographic method for determination of amino acid levels in human serum. Clin Chim Acta105:201–211 [CrossRef][PubMed]
    [Google Scholar]
  8. Groth I., Schumann P., Rainey F. A., Martin K., Schuetze B., Augsten K.. 1997; Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol47:1129–1133 [CrossRef][PubMed]
    [Google Scholar]
  9. Jin L., Lee H. G., Ko S. R., Ahn C. Y., Oh H. M.. 2015; Jatrophihabitans fulvus sp. nov., an actinobacterium isolated from grass soil. Int J Syst Evol Microbiol65:3476–3480 [CrossRef][PubMed]
    [Google Scholar]
  10. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim S.-J., Moon J.-Y., Lim J.-M., Hamada M., Ahn J.-H., Weon H.-Y., Suzuki K., Kwon S. W.. 2015; Jatrophihabitans soli sp. nov., isolated from soil. Int J Syst Evol Microbiol65:1759–1763 [CrossRef][PubMed]
    [Google Scholar]
  12. Kimura M.. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  13. Kimura M.. 1983; The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press;[CrossRef]
    [Google Scholar]
  14. Kluge A. G., Farris J. S.. 1969; Quantitative phyletics and the evolution of anurans. Syst Zool18:1–32[CrossRef]
    [Google Scholar]
  15. Kroppenstedt R. M.. 1985; Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series)vol. 20 , pp.173–199 Edited by Goodfellow M., Minnikin D. E.. New York: Academic Press;
    [Google Scholar]
  16. 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 Microbiol57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  17. MacKenzie S. L.. 1987; Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem70:151–160[PubMed]
    [Google Scholar]
  18. Madhaiyan M., Hu C. J., Kim S. J., Weon H. Y., Kwon S. W., Ji L.. 2013; Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L. Int J Syst Evol Microbiol63:1241–1248 [CrossRef][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 Surg130:341–346 [CrossRef][PubMed]
    [Google Scholar]
  20. Marmur J., Doty P.. 1962; Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol5:109–118 [CrossRef][PubMed]
    [Google Scholar]
  21. Meier A., Kirschner P., Schröder K. H., Wolters J., Kroppenstedt R. M., Böttger E. C.. 1993; Mycobacterium intermedium sp. nov. Int J Syst Bacteriol43:204–209 [CrossRef][PubMed]
    [Google Scholar]
  22. 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 Methods2:233–241 [CrossRef]
    [Google Scholar]
  23. Morris E. J., van Gylswyk N. O.. 1980; Comparison of the action of rumen bacteria on cell walls from Eragrostics tef. J Agricul Sci95:313–323[CrossRef]
    [Google Scholar]
  24. Normand P., Benson D. R.. 2012; Family IV. Geodermatophilaceae Normand 2006, 2277VP (Effective publication: Normand, orso, cournoyer, jeannin, chapelon, dawson, evtushenko and misra 1996, 8.). In Bergey’s Manual of Systematic Bacteriologyvol. 5 , p.528 Edited by Whitman W. B., Parte A., Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M. E., Ludwig W., Suzuki K.. New York: Springer;
    [Google Scholar]
  25. Qin S., Xing K., Jiang J. H., Xu L. H., Li W. J.. 2011; Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol89:457–473 [CrossRef][PubMed]
    [Google Scholar]
  26. Reinhold-Hurek B., Hurek T., Claeyssens M., van Montagu M.. 1993; Cloning, expression in Escherichia coli, and characterization of cellulolytic enzymes of Azoarcus sp., a root-invading diazotroph. J Bacteriol175:7056–7065[PubMed]
    [Google Scholar]
  27. Saitou N., Nei M.. 1987; The neighbor–joining method: a new method for reconstructing phylogenetic trees. Mol BiolEvol4:406–425
    [Google Scholar]
  28. Schleifer K. H., Kandler O.. 1972; Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev36:407–477[PubMed]
    [Google Scholar]
  29. Sen A., Daubin V., Abrouk D., Gifford I., Berry A. M., Normand P.. 2014; Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol64:3821–3832 [CrossRef][PubMed]
    [Google Scholar]
  30. Smibert R. M., Krieg N. L.. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology , pp.607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  31. 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 Evol Microbiol44:846–849 [CrossRef]
    [Google Scholar]
  32. Sun H. M., Zhang T., Yu L. Y., Sen K., Zhang Y. Q.. 2015; Ubiquity, diversity and physiological characteristics of Geodermatophilaceae in shapotou National desert ecological reserve. Front Microbiol6:1059 [CrossRef][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 Evol28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  34. 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. et al. 1987; International committee on systematic bacteriology. report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol37:463–464[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001296
Loading
/content/journal/ijsem/10.1099/ijsem.0.001296
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month

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