1887

Abstract

A short rod-shaped Gram-stain-positive actinobacterium was isolated as an endophyte from the tissues of cv. KB27 and was investigated by means of a polyphasic taxonomic approach. An analysis of its 16S rRNA gene sequence indicated that strain S9-650 forms an individual line of descent and is related to certain members of the suborder , order (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genera (family ) and (family ) and the other by members of the genera , and (family ). The organism had -diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The acyl type was found to be -glycolylated. The major menaquinone was MK-9(H) and the fatty acid profile was characterized by the predominance of iso-C, Cω9, anteiso-C and Cω8 The polar lipids comprised diphosphatidylglycerol, an unidentified glycolipid, phospholipids and aminolipids. The G+C content of the genomic DNA was 71.2 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder indicate that strain S9-650 represents a novel species in a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain of the type species is S9-650 ( = DSM 45627 = KACC 16232).

Funding
This study was supported by the:
  • , Temasek Foundation
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.039685-0
2013-04-01
2020-07-12
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/4/1241.html?itemId=/content/journal/ijsem/10.1099/ijs.0.039685-0&mimeType=html&fmt=ahah

References

  1. Ahrens R., Moll G. ( 1970 ). Ein neues knospendes Bakterium aus der Ostee. . Arch Mikrobiol 70, 243265 (in German). [CrossRef] [PubMed]
    [Google Scholar]
  2. Atlas R. ( 1997 ). Principles of Microbiology. New York, NY:: WCB McGrill-Hill;.
    [Google Scholar]
  3. Becking J. H. ( 1970 ). Frankiaceae fam. nov. (Actinomycetales) with one new combination and six new species of the genus Frankia Brunchorst 1887, 174. . Int J Syst Bacteriol 20, 201220. [CrossRef]
    [Google Scholar]
  4. Bérdy J. ( 2005 ). Bioactive microbial metabolites. . J Antibiot (Tokyo) 58, 126. [CrossRef] [PubMed]
    [Google Scholar]
  5. Bozzola J. J., Russell L. D. ( 1998 ). Electron Microscopy, , 2nd edn.. Sudbury, MS:: Jones & Bartlett;.
    [Google Scholar]
  6. Breznak J. A., Costilow R. N. ( 1994 ). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, pp. 137154. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  7. Brunchorst J. ( 1886 ). Über einige Wurzelanschwellungen besonders diejenigen von Alnus und den Elaeagnaceen. . Bot Inst Tubingen 2, 151177 (in German).
    [Google Scholar]
  8. Carlsohn M. R., Groth I., Tan G. Y. A., Schütze B., Saluz H.-P., Munder T., Yang J., Wink J., Goodfellow M. ( 2007 ). Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine. . Int J Syst Evol Microbiol 57, 16401646. [CrossRef] [PubMed]
    [Google Scholar]
  9. Collins M. D., Faulkner M., Keddie R. M. ( 1984 ). Menaquinone composition of some spore forming actinomycetes. . Syst Appl Microbiol 5, 2029. [CrossRef]
    [Google Scholar]
  10. DeLong E. F. ( 1992 ). Archaea in coastal marine environments. . Proc Natl Acad Sci U S A 89, 56855689. [CrossRef] [PubMed]
    [Google Scholar]
  11. Demain A. L. ( 1998 ). Microbial natural products: alive and well in 1998. . Nat Biotechnol 16, 34. [CrossRef] [PubMed]
    [Google Scholar]
  12. DSMZ (2001). Catalogue of Strains, 7th edn. Braunschweig: Deutsche Sammlung von Mikroorganismen und Zelkuturen.
  13. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [CrossRef] [PubMed]
    [Google Scholar]
  14. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [CrossRef]
    [Google Scholar]
  15. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [CrossRef]
    [Google Scholar]
  16. Garrity G. M., Lilburn T. G., Cole J. R., Harrison S. H., Euzéby J., Tindall B. J. ( 2007 ). The Bacteria: phylum Actinobacteria: class “Actinobacteria”. The Taxonomic Outline of Bacteria and Archaea Part 10. Release 7.7. . http://www.taxonomicoutline.org/index.php/toba/article/view/187/219
  17. Gtari M., Ghodhbane-Gtari F., Nouioui I., Beauchemin N., Tisa L. S. ( 2012 ). Phylogenetic perspectives of nitrogen-fixing actinobacteria. . Arch Microbiol 194, 311. [CrossRef] [PubMed]
    [Google Scholar]
  18. Hahn D., Lechevalier M. P., Fischer A., Stackebrandt E. ( 1989 ). Evidence for a close phylogenetic relationship between members of the genera Frankia, Geodermatophilus and Blastococcus and emendation of the family Frankiaceae. . Syst Appl Microbiol 11, 236242. [CrossRef]
    [Google Scholar]
  19. 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, 716721. [CrossRef] [PubMed]
    [Google Scholar]
  20. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [CrossRef] [PubMed]
    [Google Scholar]
  21. Krieg N. R., Padgett P. J. ( 2011 ). Phenotypic and physiological characterization methods. . Methods Microbiol 38, 1560. [CrossRef]
    [Google Scholar]
  22. Kroppenstedt R. M. ( 1985 ). Fatty acid and menaquinone analysis of actinomycetes and related organisms. . In Chemical Methods in Bacterial Systematics (SAB Technical Series no. 20) , pp. 173199. Edited by Goodfellow M., Minnikin D. E. . London:: Academic Press;.
    [Google Scholar]
  23. Kumar S., Tamura K., Nei M. ( 2004 ). MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. . Brief Bioinform 5, 150163. [CrossRef] [PubMed]
    [Google Scholar]
  24. Lechevalier M. P. ( 1994 ). Taxonomy of the genus Frankia (Actinomycetales). . Int J Syst Bacteriol 44, 18. [CrossRef]
    [Google Scholar]
  25. Lechevalier H. A., Lechevalier M. P. ( 1967 ). Biology of actinomycetes. . Annu Rev Microbiol 21, 71100. [CrossRef] [PubMed]
    [Google Scholar]
  26. Lechevalier M. P., Lechevalier H. A., Holbert P. E. ( 1968 ). Sporichthya, un nouveau genre de Streptomycetaceae . . Ann Inst Pasteur (Paris) 114, 277286 (in French).[PubMed]
    [Google Scholar]
  27. Luedemann G. M. ( 1968 ). Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). . J Bacteriol 96, 18481858.[PubMed]
    [Google Scholar]
  28. Luedemann G. M., Fonseca A. F. ( 1989 ). Genus Geodermatophilus Luedemann 1968, 1857AL . . In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 24062409. Edited by Williams S. T., Sharpe M. E., Holt J. G. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  29. Maszenan A. M., Tay J.-H., Schumann P., Jiang H.-L., Tay S. T.-L. ( 2005 ). Quadrisphaera granulorum gen. nov., sp. nov., a Gram-positive polyphosphate-accumulating coccus in tetrads or aggregates isolated from aerobic granules. . Int J Syst Evol Microbiol 55, 17711777. [CrossRef] [PubMed]
    [Google Scholar]
  30. Mergeay M., Nies D., Schlegel H. G., Gerits J., Charles P., Van Gijsegem F. ( 1985 ). Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. . J Bacteriol 162, 328334. [CrossRef] [PubMed]
    [Google Scholar]
  31. Mesbah M., Premachandran U., Whitman W. B. ( 1989 ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39, 159167. [CrossRef]
    [Google Scholar]
  32. Mevs U., Stackebrandt E., Schumann P., Gallikowski C. A., Hirsch P. ( 2000 ). Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains). . Int J Syst Evol Microbiol 50, 337346. [CrossRef] [PubMed]
    [Google Scholar]
  33. 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, 233241. [CrossRef]
    [Google Scholar]
  34. Mirza M. S., Janse J. D., Hahn D., Akkermans A. D. L. ( 1991 ). Identification of atypical Frankia strains by fatty acid analysis. . FEMS Microbiol Lett 83, 9198. [CrossRef]
    [Google Scholar]
  35. Mohagheghi A., Grohmann K., Himmel M., Leighton L., Updegraff D. M. ( 1986 ). Isolation and characterization of Acidothermus cellulolyticus gen. nov., sp. nov., a new genus of thermophilic, acidophilic, cellulolytic bacteria. . Int J Syst Bacteriol 36, 435443. [CrossRef]
    [Google Scholar]
  36. Normand P., Orso S., Cournoyer B., Jeannin P., Chapelon C., Dawson J., Evtushenko L., Misra A. K. ( 1996 ). Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae . . Int J Syst Bacteriol 46, 19. [CrossRef] [PubMed]
    [Google Scholar]
  37. Pagani H., Parenti F. ( 1978 ). Kineosporia, a new genus of the order Actinomycetales . . Int J Syst Bacteriol 28, 401406. [CrossRef]
    [Google Scholar]
  38. Pankratov T. A., Dedysh S. N., Zavarzin G. A. ( 2006 ). The leading role of actinobacteria in aerobic cellulose degradation in Sphagnum peat bogs. . Dokl Biol Sci 410, 428430. [CrossRef] [PubMed]
    [Google Scholar]
  39. Rainey F. A., Schumann P., Prauser H., Toalster R., Stackebrandt E. ( 1993 ). Sporichthya polymorpha represents a novel line of descent within the order Actinomycetales . . FEMS Microbiol Lett 109, 263267. [CrossRef]
    [Google Scholar]
  40. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  41. Santos C. L., Vieira J., Tavares F., Benson D. R., Tisa L. S., Berry A. M., Moradas-Ferreira P., Normand P. ( 2008 ). On the nature of fur evolution: a phylogenetic approach in Actinobacteria. . BMC Evol Biol 8, 185. [CrossRef] [PubMed]
    [Google Scholar]
  42. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
  43. Schrempf H. ( 2001 ). Recognition and degradation of chitin by streptomycetes. . Antonie van Leeuwenhoek 79, 285289. [CrossRef] [PubMed]
    [Google Scholar]
  44. Schumann P. ( 2011 ). Peptidoglycan structure. . Methods Microbiol 38, 101129. [CrossRef] [PubMed]
    [Google Scholar]
  45. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. ( 1997 ). Proposal for a new hierarchic classification system, Actinobacteria classis nov.. Int J Syst Bacteriol 47, 479491. [CrossRef]
    [Google Scholar]
  46. Tamura T., Hayakawa M., Hatano K. ( 1998 ). A new genus of the order Actinomycetales, Cryptosporangium gen. nov., with descriptions of Cryptosporangium arvum sp. nov. and Cryptosporangium japonicum sp. nov.. Int J Syst Bacteriol 48, 9951005. [CrossRef] [PubMed]
    [Google Scholar]
  47. Tamura T., Hayakawa M., Hatano K. ( 1999 ). Sporichthya brevicatena sp. nov.. Int J Syst Bacteriol 49, 17791784. [CrossRef] [PubMed]
    [Google Scholar]
  48. 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 Evol 28, 27312739. [CrossRef] [PubMed]
    [Google Scholar]
  49. Tao T.-S., Yue Y.-Y., Chen W.-X., Chen W.-F. ( 2004 ). Proposal of Nakamurella gen. nov. as a substitute for the bacterial genus Microsphaera Yoshimi et al. 1996, and Nakamurellaceae fam. nov. as a substitute for the illegitimate bacterial family Microsphaeraceae Rainey et al. 1997. . Int J Syst Evol Microbiol 54, 9991000. [CrossRef] [PubMed]
    [Google Scholar]
  50. Uchida K., Aida K. ( 1984 ). An improved method for the glycolate test for simple identification of acyl type of bacterial cell walls. . J Gen Appl Microbiol 30, 131134. [CrossRef] [PubMed]
    [Google Scholar]
  51. Urzì C., Salamone P., Schumann P., Rohde M., Stackebrandt E. ( 2004 ). Blastococcus saxobsidens sp. nov., and emended descriptions of the genus Blastococcus Ahrens and Moll 1970 and Blastococcus aggregatus Ahrens and Moll 1970. . Int J Syst Evol Microbiol 54, 253259. [CrossRef] [PubMed]
    [Google Scholar]
  52. Whittenbury R., Phillips K. C., Wilkinson J. F. ( 1970 ). Enrichment, isolation and some properties of methane-utilizing bacteria. . J Gen Microbiol 61, 205218. [CrossRef] [PubMed]
    [Google Scholar]
  53. Wilson K. ( 1997 ). Preparation of genomic DNA from bacteria. , pp. 2.4.12.4.5. In Current Protocols in Molecular Biology, pp. 2.4.1–2.4.5. Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. . New York:: John Wiley;.
  54. Yokota A., Tamura T., Nishii T., Hasegawa T. ( 1993 ). Kineococcus aurantiacus gen. nov., sp. nov., a new aerobic, Gram-positive, motile coccus with meso-diaminopimelic acid and arabinogalactan in the cell wall. . Int J Syst Bacteriol 43, 5257. [CrossRef]
    [Google Scholar]
  55. Yoon J.-H., Kang S.-J., Jung S.-Y., Oh T.-K. ( 2007 ). Humicoccus flavidus gen. nov., sp. nov., isolated from soil. . Int J Syst Evol Microbiol 57, 5659. [CrossRef] [PubMed]
    [Google Scholar]
  56. Yoshimi Y., Hiraishi A., Nakamura K. ( 1996 ). Isolation and characterization of Microsphaera multipartida gen. nov., sp. nov., a polysaccharide-accumulating Gram-positive bacterium from activated sludge. . Int J Syst Bacteriol 46, 519525. [CrossRef]
    [Google Scholar]
  57. Zhang Y.-Q., Chen J., Liu H.-Y., Zhang Y.-Q., Li W.-J., Yu L.-Y. ( 2011 ). Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant. . Int J Syst Evol Microbiol 61, 190193. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.039685-0
Loading
/content/journal/ijsem/10.1099/ijs.0.039685-0
Loading

Data & Media loading...

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