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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 66, Issue 12

sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle ( L.) Free

Abstract

A novel actinobacterium, designated strain NEAU-QY3, was isolated from the leaves of L. and examined using a polyphasic taxonomic approach. The organism formed single spores with smooth surface on substrate mycelia. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain had a close association with the genus and shared the highest sequence similarity with RtIII47 (99.17 %), an association that was supported by a bootstrap value of 94 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. The strain also showed high 16S rRNA gene sequence similarities to NEAU-J5 (98.78 %), 202201 (98.51 %), LK2-10 (98.28 %), YIM 013 (98.23 %) and CNR-114 (98.23 %). Furthermore, phylogenetic analysis based on the gene sequences supported the conclusion that strain NEAU-QY3 should be assigned to the genus . However, the DNA–DNA hybridization relatedness values between strain NEAU-QY3 and RtIII47 and YIM 013 were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results, strain NEAU-QY3 was readily distinguished from its most closely related strains and classified as a new species, for which the name sp. nov. is proposed. The type strain is NEAU-QY3 (=CGMCC 4.7312=DSM 101530).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , gyrB gene , Polyphasic taxonomy , Sonchus oleraceus L and Verrucosispora sonchi sp. nov.
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2016-12-01
2025-04-21
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References

  1. Ahmed L., Jensen P. R., Freel K. C., Brown R., Jones A. L., Kim B. Y., Goodfellow M. 2013; Salinispora pacifica sp. nov., an actinomycete from marine sediments. Antonie van Leeuwenhoek 103:1069–1078 [View Article][PubMed]
     [Google Scholar]
  2. Bister B., Bischoff D., Ströbele M., Riedlinger J., Reicke A., Wolter F., Bull A. T., Zähner H., Fiedler H. P., Süssmuth R. D. 2004; Abyssomicin C-A polycyclic antibiotic from a marine Verrucosispora strain as an inhibitor of the p-aminobenzoic acid/tetrahydrofolate biosynthesis pathway. Angew Chem Int Ed Engl 43:2574–2576 [View Article][PubMed]
     [Google Scholar]
  3. Collins M. D. 1985; Isoprenoid quinone analyses in bacterial classification and identification. In Chemical Methods in Bacterial Systematics pp. 267–284 Edited by Goodfellow M., Minnikin D. E. London: Academic Press;
     [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 39:783–789 [View Article]
     [Google Scholar]
  7. Gao R. X., Liu C. X., Zhao J. W., Jia F. Y., Yu C., Yang L. Y., Wang X. J., Xiang W. S. 2014; Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora . Antonie van Leeuwenhoek 105:307–315 [View Article][PubMed]
     [Google Scholar]
  8. Garcia L. C., Martínez-Molina E., Trujillo M. E. 2010; Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum . Int J Syst Evol Microbiol 60:331–337 [View Article][PubMed]
     [Google Scholar]
  9. Goodfellow M., Stach J. E., Brown R., Bonda A. N., Jones A. L., Mexson J., Fiedler H. P., Zucchi T. D., Bull A. T. 2012; Verrucosispora maris sp. nov., a novel deep-sea actinomycete isolated from a marine sediment which produces abyssomicins. Antonie van Leeuwenhoek 101:185–193 [View Article][PubMed]
     [Google Scholar]
  10. Goodfellow M., Brown R., Ahmed L., Pathom-Aree W., Bull A. T., Jones A. L., Stach J. E., Zucchi T. D., Zhang L. et al. 2013; Verrucosispora fiedleri sp. nov., an actinomycete isolated from a fjord sediment which synthesizes proximicins. Antonie van Leeuwenhoek 103:493–502 [View Article][PubMed]
     [Google Scholar]
  11. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H.-N. 1974; Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63 [View Article]
     [Google Scholar]
  12. Huss V. A. R., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [View Article][PubMed]
     [Google Scholar]
  13. Huyan T., Li Q., Wang Y. L., Li J., Zhang J. Y., Liu Y. X., Shahid M. R., Yang H., Li H. Q. 2016; Anti-tumor effect of hot aqueous extracts from Sonchus oleraceus (L.) L. and Juniperus sabina L – two traditional medicinal plants in China. J Ethnopharmacol 185:289–299 [View Article][PubMed]
     [Google Scholar]
  14. Keller S., Nicholson G., Drahl C., Sorensen E., Fiedler H. P., Süssmuth R. D. 2007; Abyssomicins G and H and atropabyssomicin C from the marine Verrucosispora strain AB-18-032. J Antibiot 60:391–394 [View Article][PubMed]
     [Google Scholar]
  15. 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]
  16. 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 Microbiol 62:716–721 [View Article][PubMed]
     [Google Scholar]
  17. 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]
  18. Lechevalier M. P., Lechevalier H. A. 1980; The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy, Special Publication 6 pp. 277–284 Arlington, VA: Society for Industrial Microbiology;
     [Google Scholar]
  19. Lechevalier M. P., De Bièvre C., Lechevalier H. 1977; Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260 [View Article]
     [Google Scholar]
  20. Lee Y. K., Kim H. W., Liu C. L., Lee H. K. 2003; A simple method for DNA extraction from marine bacteria that produce extracellular materials. J Microbiol Methods 52:245–250 [View Article][PubMed]
     [Google Scholar]
  21. Liao Z. L., Tang S. K., Guo L., Zhang Y. Q., Tian X. P., Jiang C. L., Xu L. H., Li W. J. 2009; Verrucosispora lutea sp. nov., isolated from a mangrove sediment sample. Int J Syst Evol Microbiol 59:2269–2273 [View Article][PubMed]
     [Google Scholar]
  22. Li Y., Chu H. Y., Li H. B., Yuan Q. 2012; Extraction and content determination of flavonoids in Sonchus oleraceus L. Medicinal Plant 3:48–50
     [Google Scholar]
  23. Liu Z. W., Zhao X. L. 2010; Effects of different extraction methods on extraction rate of polysaccharide from Sonchus oleraceus L. Medicinal Plant 1:32–35
     [Google Scholar]
  24. Loqman S., Barka E. A., Clément C., Ouhdouch Y. 2009; Antagonistic actinomycetes from Moroccan soil to control the grapevine gray mold. World J Microbiol Biotechnol 25:81–91 [View Article]
     [Google Scholar]
  25. Mandel M., Marmur J. 1968; Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195–206 [CrossRef]
     [Google Scholar]
  26. Ma Z. X., Liu C. X., Fan J. L., He H. R., Li C., Li J. S., Zhao S. S., Xiang W. S., Wang X. J. 2015; Plantactinospora sonchi sp. nov. a novel actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.). Int J Syst Evol Microbiol 65:4895–4901 [View Article][PubMed]
     [Google Scholar]
  27. McKerrow J., Vagg S., McKinney T., Seviour E. M., Maszenan A. M., Brooks P., Seviour R. J. 2000; A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 30:178–182 [View Article][PubMed]
     [Google Scholar]
  28. Minnikin D. E., Hutchinson I. G., Caldicott A. B., Goodfellow M. 1980; Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr 188:221–233 [View Article]
     [Google Scholar]
  29. 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]
  30. Rheims H., Schumann P., Rohde M., Stackebrandt E. 1998; Verrucosispora gifhornensis gen. nov., sp. nov., a new member of the actinobacterial family Micromonosporaceae . Int J Syst Bacteriol 48:1119–1127 [View Article][PubMed]
     [Google Scholar]
  31. Riedlinger J., Reicke A., Zähner H., Krismer B., Bull A. T., Maldonado L. A., Ward A. C., Goodfellow M., Bister B. et al. 2004; Abyssomicins, inhibitors of the para-aminobenzoic acid pathway produced by the marine Verrucosispora strain AB-18-032. J Antibiot 57:271–279 [View Article][PubMed]
     [Google Scholar]
  32. 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]
  33. Schneider K., Keller S., Wolter F. E., Röglin L., Beil W., Seitz O., Nicholson G., Bruntner C., Riedlinger J. et al. 2008; Proximicins A, B, and C-antitumor furan analogues of netropsin from the marine actinomycete Verrucosispora induce upregulation of p53 and the cyclin kinase inhibitor p21. Angew Chem Int Ed Engl 47:3258–3261 [View Article][PubMed]
     [Google Scholar]
  34. Shirai M., Okuda M., Motohashi K., Imoto M., Furihata K., Matsuo Y., Katsuta A., Shizuri Y., Seto H. 2010; Terpenoids produced by actinomycetes: isolation, structural elucidation and biosynthesis of new diterpenes, gifhornenolones A and B from Verrucosispora gifhornensis YM28-088. J Antibiot (Tokyo) 63:245–250 [View Article][PubMed]
     [Google Scholar]
  35. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int Syst Bacteriol 16:313–340 [View Article]
     [Google Scholar]
  36. Smibert R. M., Krieg N. R. 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]
  37. Supong K., Suriyachadkun C., Pittayakhajonwut P., Suwanborirux K., Thawai C. 2013; Micromonospora spongicola sp. nov., an actinomycete isolated from a marine sponge in the Gulf of Thailand. J Antibiot 66:505–509 [View Article][PubMed]
     [Google Scholar]
  38. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  39. Thawai C., Tanasupawat S., Itoh T., Suwanborirux K., Suzuki K., Kudo T. 2005; Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest. Int J Syst Evol Microbiol 55:417–422 [View Article][PubMed]
     [Google Scholar]
  40. Uchida K., Kudo T., Suzuki K., Nakase T. 1999; A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 45:49–56 [View Article][PubMed]
     [Google Scholar]
  41. Waksman S. A. 1961 The Actinomycetes, vol. 2, Classification, Identification and Descriptions of Genera and Species Baltimore: Williams & Wilkins;
     [Google Scholar]
  42. Waksman S. A. 1967 The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press;
     [Google Scholar]
  43. Wang X., Jia F., Liu C., Zhao J., Wang L., Shen Y., Wang J., Zhang J., Li C. et al. 2013; Xiangella phaseoli gen. nov., sp. nov., a member of the family Micromonosporaceae . Int J Syst Evol Microbiol 63:2138–2145 [View Article][PubMed]
     [Google Scholar]
  44. 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 Bacteriol 37:463–464 [View Article]
     [Google Scholar]
  45. Wu C., Lu X., Qin M., Wang Y., Ruan J. 1989; Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 16:176–178
     [Google Scholar]
  46. Xi L., Zhang L., Ruan J., Huang Y. 2012; Description of Verrucosispora qiuiae sp. nov., isolated from mangrove swamp sediment, and emended description of the genus Verrucosispora . Int J Syst Evol Microbiol 62:1564–1569 [View Article][PubMed]
     [Google Scholar]
  47. Xiang W. S., Liu C. X., Wang X. J., Du J., Xi L. J., Huang Y. 2011; Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 61:1165–1169 [View Article][PubMed]
     [Google Scholar]
  48. Xie Q. Y., Wang C., Wang R., Qu Z., Lin H. P., Goodfellow M., Hong K. 2011; Jishengella endophytica gen. nov., sp. nov., a new member of the family Micromonosporaceae . Int J Syst Evol Microbiol 61:1153–1159 [View Article][PubMed]
     [Google Scholar]
  49. 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]
  50. Yokota A., Tamura T., Hasegawa T., Huang L. H. 1993; Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales . Int J Syst Bacteriol 43:805–812 [View Article]
     [Google Scholar]
  51. Yu C., Liu C. X., Wang X. J., Zhao J. W., Yang L. Y., Gao R. X., Zhang Y. J., Xiang W. S. 2013; Streptomyces polyrhachii sp. nov., a novel actinomycete isolated from the edible Chinese black ant (Polyrhachis vicina Roger). Antonie van Leeuwenhoek 104:1013–1019 [View Article][PubMed]
     [Google Scholar]
  52. Zhao D., Ding Q., Xiao Y. 2009; Study progress of dahurian patrinia herb. Guiding Journal of Traditional Chinese Medicine and Pharmacy 10:76–78
     [Google Scholar]
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Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.)
Int J Syst Evol Microbiol 66, 5430 (2016); https://doi.org/10.1099/ijsem.0.001537
/content/journal/ijsem/10.1099/ijsem.0.001537
/content/journal/ijsem/10.1099/ijsem.0.001537
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