1887

Abstract

A Gram-stain-positive actinobacterium, designated strain YIM DR4008, was isolated from the root sample of collected from Lijiang, Yunnan, China. Strain YIM DR4008 could grow at temperatures ranging from 10 to 50 °C (optimum 28–30 °C), at pH 5.0–11.0 (optimum pH 7.0) and in the presence of up to 4 % (w/v) NaCl. Sequence analysis of the 16S ribosomal RNA gene revealed that strain YIM DR4008 shared highest similarity (95.0 %) with NBRC 12779 and <95 % similarity with other known members of the genera , and The diagnostic cell-wall diamino acid of strain YIM DR4008 was found to be -diaminopimelic acid. The whole-cell hydrolysates contained a major amount of galactose and mannose along with a small proportion of fucose, glucose, rhamnose and ribose. The polar lipids consisted of diphosphatidylglycerol, phosphatidylinositol mannosides and three unidentified phospholipids. The respiratory menaquinones were MK-9(H) and MK-9(H), while the major cellular fatty acids (>10 %) were anteiso-C, C, iso-C, iso-C and anteiso-C. The genomic DNA G+C content was determined to be 75.3 mol%. Based on the phenotypic, chemotaxonomic and molecular characteristics, strain YIM DR4008 is proposed to be recognized as a novel species of a new genus in the family , with the name gen. nov., sp. nov. The type strain of the type species is YIM DR4008 (=DSM 42178=CGMCC 4.7247). An emended description of the family is also provided.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001617
2017-02-01
2020-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/2/288.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001617&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. Zhang Z, Wang Y, Ruan J. A proposal to revive the genus Kitasatospora (Omura, Takahashi, Iwai, and Tanaka 1982). Int J Syst Bacteriol 1997;47:1048–1054 [CrossRef][PubMed]
    [Google Scholar]
  3. Kim SB, Lonsdale J, Seong CN, Goodfellow M. Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943)AL) emend. Rainey et al. 1997. Antonie van Leeuwenhoek 2003;83:107–116[PubMed][CrossRef]
    [Google Scholar]
  4. Qin S, Xing K, Jiang JH, Xu LH, Li WJ. Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol 2011;89:457–473 [CrossRef][PubMed]
    [Google Scholar]
  5. Liu Z, Rodríguez C, Wang L, Cui Q, Huang Y et al. Kitasatospora viridis sp. nov., a novel actinomycete from soil. Int J Syst Evol Microbiol 2005;55:707–711 [CrossRef][PubMed]
    [Google Scholar]
  6. Zhang BH, Cheng J, Li L, Zhang YG, Wang HF et al. Streptomyces jiujiangensis sp. nov., isolated from soil in South China. Antonie van Leeuwenhoek 2014;105:763–770 [CrossRef][PubMed]
    [Google Scholar]
  7. Groth I, Rodríguez C, Schütze B, Schmitz P, Leistner E et al. Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 2004;54:2121–2129 [CrossRef][PubMed]
    [Google Scholar]
  8. Golinska P, Ahmed L, Wang D, Goodfellow M. Streptacidiphilus durhamensis sp. nov., isolated from a spruce forest soil. Antonie van Leeuwenhoek 2013;104:199–206 [CrossRef][PubMed]
    [Google Scholar]
  9. Hozzein WN, Goodfellow M. Streptomyces synnematoformans sp. nov., a novel actinomycete isolated from a sand dune soil in Egypt. Int J Syst Evol Microbiol 2007;57:2009–2013 [CrossRef][PubMed]
    [Google Scholar]
  10. Sharma TK, Mawlankar R, Sonalkar VV, Shinde VK, Zhan J et al. Streptomyces lonarensis sp. nov., isolated from Lonar Lake, a meteorite salt water lake in India. Antonie van Leeuwenhoek 2016;109:225–235 [CrossRef][PubMed]
    [Google Scholar]
  11. Veyisoglu A, Sahin N. Streptomyces hoynatensis sp. nov., isolated from deep marine sediment. Int J Syst Evol Microbiol 2014;64:819–826 [CrossRef][PubMed]
    [Google Scholar]
  12. Zhang L, Wang Y, Wei L, Wang Y, Shen X et al. Taibaiella milacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus. Int J Syst Evol Microbiol 2013;63:3769–3776 [CrossRef][PubMed]
    [Google Scholar]
  13. Liu N, Wang H, Liu M, Gu Q, Zheng W et al. Streptomyces alni sp. nov., a daidzein-producing endophyte isolated from a root of Alnus nepalensis D. Don. Int J Syst Evol Microbiol 2009;59:254–258 [CrossRef][PubMed]
    [Google Scholar]
  14. Bian GK, Qin S, Yuan B, Zhang YJ, Xing K et al. Streptomyces phytohabitans sp. nov., a novel endophytic actinomycete isolated from medicinal plant Curcuma phaeocaulis. Antonie van Leeuwenhoek 2012;102:289–296 [CrossRef][PubMed]
    [Google Scholar]
  15. Li J, Zhao GZ, Zhu WY, Huang HY, Xu LH et al. Streptomyces endophyticus sp. nov., an endophytic actinomycete isolated from Artemisia annua L. Int J Syst Evol Microbiol 2013;63:224–229 [CrossRef][PubMed]
    [Google Scholar]
  16. Li J, Zhao GZ, Chen HH, Wang HB, Qin S et al. Antitumour and antimicrobial activities of endophytic streptomycetes from pharmaceutical plants in rainforest. Lett Appl Microbiol 2008;47:574–580 [CrossRef][PubMed]
    [Google Scholar]
  17. Khieu TN, Liu MJ, Nimaichand S, Quach NT, Chu-Ky S et al. Characterization and evaluation of antimicrobial and cytotoxic effects of Streptomyces sp. HUST012 isolated from medicinal plant Dracaena cochinchinensis Lour. Front Microbiol 2015;6:574 [CrossRef][PubMed]
    [Google Scholar]
  18. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  19. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. 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 2007;57:1424–1428 [CrossRef][PubMed]
    [Google Scholar]
  20. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  21. 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]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425[PubMed]
    [Google Scholar]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  25. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  26. 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]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–789 [CrossRef]
    [Google Scholar]
  28. 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]
  29. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  30. Tang SK, Wang Y, Chen Y, Lou K, Cao LL et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 2009;59:2025–2032 [CrossRef][PubMed]
    [Google Scholar]
  31. 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 [CrossRef]
    [Google Scholar]
  32. 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 [CrossRef]
    [Google Scholar]
  33. 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]
  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. 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]
  36. Hu HY, Lim BR, Goto N, Fujie K. Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples. J Microbiol Methods 2001;47:17–24 [CrossRef][PubMed]
    [Google Scholar]
  37. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990;20:16
    [Google Scholar]
  38. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989;39:159–167 [CrossRef]
    [Google Scholar]
  39. Waksman SA. The Actinomycetes: A Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  40. 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]
  41. 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 [CrossRef][PubMed]
    [Google Scholar]
  42. 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]
  43. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriologyvol. 4 Baltimore: Williams & Willkins; 1989; pp2453–2492
    [Google Scholar]
  44. Athalye M, Goodfellow M, Lacey J, White RP. Numerical classification of Actinomadura and Nocardiopsis. Int J Syst Bacteriol 1985;35:86–98 [CrossRef]
    [Google Scholar]
  45. Pridham TG, Gottlieb D. The utilization of carbon compounds by some Actinomycetales as an aid for species determination. J Bacteriol 1948;56:107–114[PubMed]
    [Google Scholar]
  46. Nie GX, Ming H, Li S, Zhou EM, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012;62:2650–2656 [CrossRef][PubMed]
    [Google Scholar]
  47. Zhi X-Y, Li W-J, Stackebrandt E. An update of the structure and 16s rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009;59:589–608 [CrossRef]
    [Google Scholar]
  48. Kämpfer P. Streptomycetaceae In Whitman WB. (editor) Bergey’s Manual of Systematic of Archaea and Bacteria Wiley Online Library; 2015; pp1–11[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001617
Loading
/content/journal/ijsem/10.1099/ijsem.0.001617
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