1887

Abstract

A novel endophytic actinobacterium strain, designated A249, was isolated from the stem of Populus adenopoda collected at Mount Qingcheng in south-west China. Its taxonomic position was determined by using a polyphasic approach. The cultural and morphological characteristics of isolate A249 were consistent with members of the genus Streptomyces. Growth occurred at 10–37 °C, pH 6.0–12.0 and in the presence of 0–4 % (w/v) NaCl. Analysis of the 16S rRNA gene sequence and phylogenetic trees showed the closest phylogenetic relatives to strain A249 were Streptomyces shaanxiensis JCM 16925 (98.0 % 16S rRNA gene sequence similarity) and Streptomyces lanatus JCM 4332 (97.9 %). The DNA–DNA hybridization values between the strain A249 and the two reference strains ranged from 41.4 to 49.4 %. The DNA G+C content was 71.7 mol%. The range of average nucleotide identity values was 81.5–86.7 %. Chemical analysis of cellular components indicated that strain A249 contained ll-diaminopimelic acid, xylose and galactose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The polar lipids were diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylethanolamine, two unidentified lipids, one unidentified phospholipid, one unidentified aminolipid and one unidentified aminophospholipid. The major fatty acids comprised C16 : 0, iso-C14 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and C16 : 1ω7c. On the basis of the phenotypic and genotypic differentiation of the three tested strains, isolate A249 is proposed to represent a novel species of the genus Streptomyces, named Streptomyces populi sp. nov. The type strain is A249 (=CGMCC 4.7417=JCM 32175).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002877
2018-06-26
2020-05-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/8/2568.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002877&mimeType=html&fmt=ahah

References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943;46:337–341[PubMed]
    [Google Scholar]
  2. Bascom-Slack CA, Ma C, Moore E, Babbs B, Fenn K et al. Multiple, novel biologically active endophytic actinomycetes isolated from upper Amazonian rainforests. Microb Ecol 2009;58:374–383 [CrossRef][PubMed]
    [Google Scholar]
  3. Kaewkla O, Franco CMM. Streptomyces roietensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of jasmine rice, Oryza sativa KDML 105. Int J Syst Evol Microbiol 2017;67:4868–4872 [CrossRef][PubMed]
    [Google Scholar]
  4. Köberl M, Schmidt R, Ramadan EM, Bauer R, Berg G. The microbiome of medicinal plants: diversity and importance for plant growth, quality and health. Front Microbiol 2013;4:400 [CrossRef][PubMed]
    [Google Scholar]
  5. Lodewyckx C, Vangronsveld J, Porteous F, Moore ERB, Taghavi S et al. Endophytic bacteria and their potential applications. CRC Crit Rev Plant Sci 2002;21:583–606 [CrossRef]
    [Google Scholar]
  6. 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]
  7. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 1987;65:501–509 [CrossRef]
    [Google Scholar]
  8. Crawford DL, Lynch JM, Whipps JM, Ousley MA. Isolation and characterization of actinomycete antagonists of a fungal root pathogen. Appl Environ Microbiol 1993;59:3899–3905[PubMed]
    [Google Scholar]
  9. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  10. Nikodinovic J, Barrow KD, Chuck JA. High yield preparation of genomic DNA from Streptomyces. Biotechniques 2003;35:932–936[PubMed]
    [Google Scholar]
  11. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  12. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  16. 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]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  18. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970;12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  19. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983;4:184–192 [CrossRef][PubMed]
    [Google Scholar]
  20. 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]
  21. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983;129:1743–1813 [CrossRef][PubMed]
    [Google Scholar]
  22. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  24. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  25. Waksman SA. A summary of current knowledge. In The Actinomycetes New York: Ronald Press; 1967
    [Google Scholar]
  26. Waksman SA. Classification, identification and descriptions of genera and species. In Actinomycetes, 2nd ed. Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  27. Kelly KL. Inter-Society Color Council–National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  28. Long X, Liu B, Zhang S, Zhang Y, Zeng Z et al. Sphingobacterium griseoflavum sp. nov., isolated from the insect Teleogryllus occipitalis living in deserted cropland. Int J Syst Evol Microbiol 2016;66:1956–1961 [CrossRef][PubMed]
    [Google Scholar]
  29. 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]
  30. Mata JA, Martínez-Cánovas J, Quesada E, Béjar V. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst Appl Microbiol 2002;25:360–375 [CrossRef][PubMed]
    [Google Scholar]
  31. Barritt MM. The intensification of the Voges-Proskauer reaction by the addition of α-naphthol. J Pathol Bacteriol 1936;42:441–454 [CrossRef]
    [Google Scholar]
  32. Goodfellow M, Orchard VA. Antibiotic sensitivity of some nocardioform bacteria and its value as a criterion for taxonomy. J Gen Microbiol 1974;83:375–387 [CrossRef][PubMed]
    [Google Scholar]
  33. 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]
  34. 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]
  35. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: MIDI Inc; 1990
    [Google Scholar]
  36. Xiang W, Liu C, Wang X, Du J, Xi L et al. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 2011;61:1165–1169 [CrossRef][PubMed]
    [Google Scholar]
  37. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  38. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982;5:2359–2367 [CrossRef]
    [Google Scholar]
  39. Pridham TG, Hesseltine CW, Benedict RG. A guide for the classification of streptomycetes according to selected groups; placement of strains in morphological sections. Appl Microbiol 1958;6:52–79[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002877
Loading
/content/journal/ijsem/10.1099/ijsem.0.002877
Loading

Data & Media loading...

Supplements

Supplementary File 2

PDF

Most cited this month Most Cited RSS feed

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