1887

Abstract

A novel endophytic bacterium, designated strain SZ4R5S7, was isolated from surface-sterilized root of an endangered medicinal plant (Ferula songorica Pall. ex Spreng) collected from Xinjiang, north-west China. The taxonomic position of the strain was investigated by using a polyphasic approach. The strain was found to be aerobic, Gram-stain-positive, oxidase-negative and catalase-positive, short rods and non-motile. Strain SZ4R5S7 grew at 4–37 °C (optimum, 28 °C), pH 5.0–9.0 (pH 6.0–8.0) and in the presence of 0–4 % (w/v) NaCl. The polar lipids detected for strain SZ4R5S7 were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified lipids. The predominant menaquinone of strain SZ4R5S7 was MK-8(H4), and the major fatty acids were iso-C16 : 0 and anteiso-C14 : 0. The DNA G+C content was determined to be 72.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SZ4R5S7 belongs to the genus Nocardioides and showed highest levels of 16S rRNA gene sequence similarity to members of the strain Nocardioides kribbensis KSL-2 (97.8 %). On the basis of phenotypic, genotypic and phylogenetic data, strain SZ4R5S7 represents a novel species in the genus Nocardioides, for which the name Nocardioides ferulae sp. nov. is proposed and the type strain is SZ4R5S7 (=CGMCC 4.7456=KCTC 39994).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003261
2019-02-08
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/5/1253.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003261&mimeType=html&fmt=ahah

References

  1. Prauser H. Nocardioides, a new genus of the order actinomycetales. Int J Syst Bacteriol 1976; 26:58–65 [View Article]
    [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
    [Google Scholar]
  3. Singh H, Du J, Trinh H, Won K, Yang JE et al. Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. Int J Syst Evol Microbiol 2016; 66:371–378 [View Article][PubMed]
    [Google Scholar]
  4. Zhang LY, Ming H, Zhao ZL, Ji WL, Salam N et al. Nocardioides allogilvus sp. nov., a novel actinobacterium isolated from a karst cave. Int J Syst Evol Microbiol 2018; 68:2485–2490 [View Article][PubMed]
    [Google Scholar]
  5. Yi H, Chun J. Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2004; 54:2151–2154 [View Article][PubMed]
    [Google Scholar]
  6. Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ. Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea. Int J Syst Evol Microbiol 2008; 58:2292–2296 [View Article][PubMed]
    [Google Scholar]
  7. Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH et al. Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla). Int J Syst Evol Microbiol 2015; 65:1953–1958 [View Article][PubMed]
    [Google Scholar]
  8. Han JH, Kim TS, Joung Y, Kim MN, Shin KS et al. Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots. Int J Syst Evol Microbiol 2013; 63:4730–4734 [View Article][PubMed]
    [Google Scholar]
  9. Liu Q, Xin YH, Liu HC, Zhou YG, Wen Y. Nocardioides szechwanensis sp. nov. and Nocardioides psychrotolerans sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2013; 63:129–133 [View Article][PubMed]
    [Google Scholar]
  10. Zhang HX, Wang K, Xu ZX, Chen GJ, Du ZJ. Nocardioides gilvus sp. nov., isolated from Namtso Lake. Antonie van Leeuwenhoek 2016; 109:1367–1374 [View Article][PubMed]
    [Google Scholar]
  11. Fang BZ, Hua ZS, Han MX, Zhang ZT, Wang YH et al. Nonomuraea cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. Int J Syst Evol Microbiol 2017; 67:4692–4697 [View Article][PubMed]
    [Google Scholar]
  12. Qin S, Wang HB, Chen HH, Zhang YQ, Jiang CL et al. Glycomyces endophyticus sp. nov., an endophytic actinomycete isolated from the root of Carex baccans Nees. Int J Syst Evol Microbiol 2008; 58:2525–2528 [View Article][PubMed]
    [Google Scholar]
  13. Liu Y, Guo J, Li L, Asem MD, Zhang Y et al. Endophytic bacteria associated with endangered plant Ferula sinkiangensis K. M. Shen in an arid land: diversity and plant growth-promoting traits. J Arid Land 2017; 9:432–445 [View Article]
    [Google Scholar]
  14. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  15. RMIn A, Parks LC. (editors) Handbook of Microbiological Media, 4th ed. Boca Raton, FL: CRC Press; 2010 p. 719
    [Google Scholar]
  16. Waksman SA. The actinomycetes. A Summary of Current Knowledge New York: RonaldPress; 1967
    [Google Scholar]
  17. 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]
  18. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
    [Google Scholar]
  19. 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 [View Article]
    [Google Scholar]
  20. Williams ST, Goodfellow M, Alderson G, Waksman GS. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology vol. 4 Baltimore: Williams & Willkins; 1943 pp. 2453–2492
    [Google Scholar]
  21. Li J, Zhao GZ, Long LJ, Wang FZ, Tian XP et al. Rhodococcus nanhaiensis sp. nov., an actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 2012; 62:2517–2521 [View Article][PubMed]
    [Google Scholar]
  22. 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 [View Article][PubMed]
    [Google Scholar]
  23. 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 [View Article][PubMed]
    [Google Scholar]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  25. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  26. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  28. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  30. 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 [View Article][PubMed]
    [Google Scholar]
  31. Harrison P. SPADES - a process algebra for discrete event simulation. J Logic Comput 2000; 10:3–42 [View Article]
    [Google Scholar]
  32. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
    [Google Scholar]
  33. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article][PubMed]
    [Google Scholar]
  34. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  35. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article][PubMed]
    [Google Scholar]
  36. 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 [View Article][PubMed]
    [Google Scholar]
  37. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  38. Jurado V, Boiron P, Kroppenstedt RM, Laurent F, Couble A et al. Nocardia altamirensis sp. nov., isolated from Altamira cave, Cantabria, Spain. Int J Syst Evol Microbiol 2008; 58:2210–2214 [View Article][PubMed]
    [Google Scholar]
  39. Kämpfer P, Buczolits S, Jäckel U, Grün-Wollny I, Busse HJ. Nocardia tenerifensis sp. nov. Int J Syst Evol Microbiol 2004; 54:381–383 [View Article][PubMed]
    [Google Scholar]
  40. 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 [View Article]
    [Google Scholar]
  41. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986; 123:31–36[PubMed]
    [Google Scholar]
  42. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: Microbial ID, Inc; 1990
    [Google Scholar]
  43. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  44. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of cellulomonas, oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
    [Google Scholar]
  45. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003261
Loading
/content/journal/ijsem/10.1099/ijsem.0.003261
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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