1887

Abstract

A novel actinomycete strain, designated RP-AC37, was isolated from rhizosphere soil collected on Mara Island of Jeju, Republic of Korea. Cells were aerobic, Gram-positive, oxidase-negative, catalase-positive, non-mycelium-forming and motile rods (0.6–0.7×1.9–2.4 µm). Phylogenetic analysis based on 16S rRNA gene sequences showed that the organism formed a distinct clade within the radiation occupied by the suborder . 16S rRNA gene similarity values were less than 93.2 % to members of the suborder and related taxa. The diamino acid isomer in the cell-wall peptidoglycan was -diaminopimelic acid. The major whole-cell sugars were glucose, galactose and xylose. The major menaquinone was MK-9(H). The polar lipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The cellular fatty acids were straight-chain, unsaturated and saturated, with a significant amount of tuberculostearic acid (10-methyl-C). The DNA G+C content was 73.2 mol%. The combination of morphological, chemotaxonomic and phylogenetic data clearly separate the isolate from members of known genera of the suborder and related taxa, suggesting that the isolate represents a novel species in a new genus in this suborder, for which the name gen. nov., sp. nov. is proposed; the type strain is RP-AC37 ( = KCTC 19630 = DSM 45328).

Funding
This study was supported by the:
  • 21C Frontier Microbial Genomics and Application Center Program, Ministry of Science & Technology, Republic of Korea
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.030007-0
2012-02-01
2021-05-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/62/2/315.html?itemId=/content/journal/ijsem/10.1099/ijs.0.030007-0&mimeType=html&fmt=ahah

References

  1. Ahrens R., Moll G. 1970; Ein neues knospendes Bakterium aus der Ostee. Arch Mikrobiol 70:243–265 (in German) [CrossRef][PubMed]
    [Google Scholar]
  2. Brunchorst J. 1886; Über einige Wurzelanschwellungen besonders diejenigen von Alnus und den Elaeagnaceen. Bot Inst Tubingen 2:151–177 (in German)
    [Google Scholar]
  3. Carlsohn M. R., Groth I., Saluz H.-P., Schumann P., Stackebrandt E. 2008; Fodinicola feengrottensis gen. nov., sp. nov., an actinomycete isolated from a medieval mine. Int J Syst Evol Microbiol 58:1529–1536 [CrossRef][PubMed]
    [Google Scholar]
  4. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  5. Felsenstein J. 1993; phylip (phylogeny inference package) version 3.5.1. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  6. Fitch W. M. 1971; Towards defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [CrossRef]
    [Google Scholar]
  7. Garrity G. M., Lilburn T. G., Cole J. R., Harrison S. H., Euzéby J., Tindall B. J. 2007; The Taxonomic Outline of Bacteria and Archaea. Part 10. The Bacteria: phylum Actinobacteria, class “Actinobacteria”. TOBA Release 7.7. http://www.taxonomicoutline.org
  8. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H.-N. 1974; Nocardia coeliaca, Nocardia autotrophica, and the nocardia strain. Int J Syst Bacteriol 24:54–63 [CrossRef]
    [Google Scholar]
  9. Hopwood D. A., Bibb M. J., Chater K. F., Kieser T., Bruton C. J., Kieser H. M., Lydiate D. J., Smith C. P., Ward J. M., Schrempf H. (editors) 1985 Genetic Manipulation of Streptomyces. A Laboratory Manual Norwich: John Innes Foundation;
    [Google Scholar]
  10. Itoh T., Kudo T., Parenti F., Seino A. 1989; Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Bacteriol 39:168–173 [CrossRef]
    [Google Scholar]
  11. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism vol. 3 pp. 21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  12. Kroppenstedt R. M. 1985; Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series vol. 20) pp. 173–199 Edited by Goodfellow M., Minnikin D. E. London: Academic Press;
    [Google Scholar]
  13. Kudo T., Matsushima K., Itoh T., Sasaki J., Suzuki K.-I. 1998; Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia . Int J Syst Bacteriol 48:1245–1255 [CrossRef][PubMed]
    [Google Scholar]
  14. Lechevalier M. P. 1994; Taxonomy of the genus Frankia (Actinomycetales). Int J Syst Bacteriol 44:1–8 [CrossRef]
    [Google Scholar]
  15. Lechevalier M. P., Lechevalier H. A., Holbert P. E. 1968; Sporichthya, un nouveau genre de Streptomycetaceae . Ann Inst Pasteur (Paris) 114:277–286 (in French) [PubMed]
    [Google Scholar]
  16. Lee S. D. 2007; Marmoricola aequoreus sp. nov., a novel actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 57:1391–1395 [CrossRef][PubMed]
    [Google Scholar]
  17. Lee S. D. 2009; Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis . Int J Syst Evol Microbiol 59:1401–1404 [CrossRef][PubMed]
    [Google Scholar]
  18. Lee S. D., Park S. K., Yun Y.-W., Lee D. W. 2008; Saxeibacter lacteus gen. nov., sp. nov., an actinobacterium isolated from rock. Int J Syst Evol Microbiol 58:906–909 [CrossRef][PubMed]
    [Google Scholar]
  19. Li J., Zhao G.-Z., Huang H.-Y., Qin S., Zhu W.-Y., Xu L.-H., Li W.-J. 2009; Kineosporia mesophila sp. nov., isolated from surface-sterilized stems of Tripterygium wilfordii . Int J Syst Evol Microbiol 59:3150–3154 [CrossRef][PubMed]
    [Google Scholar]
  20. Luedemann G. M. 1968; Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). J Bacteriol 96:1848–1858[PubMed]
    [Google Scholar]
  21. Luedemann G. M., Fonseca A. F. 1989; Genus Geodermatophilus Luedemann 1968, 1857AL . In Bergey's Manual of Systematic Bacteriology vol. 4 pp. 2406–2409 Edited by Williams S. T., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  22. MacFaddin J. F. 1980 Biochemical Tests for Identification of Medical Bacteria, 2nd edn. Baltimore: Williams & Wilkins;
    [Google Scholar]
  23. 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 55:1771–1777 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 39:159–167 [CrossRef]
    [Google Scholar]
  25. 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 50:337–346 [CrossRef][PubMed]
    [Google Scholar]
  26. Minnikin D. E., Alshamaony L., Goodfellow M. 1977; Differentiation of Mycobacterium, Nocardia, and related taxa by thin layer chromatographic analysis of whole-cell methanolysates. J Gen Microbiol 88:200–204 [CrossRef]
    [Google Scholar]
  27. Minnikin D. E., Hutchinson I. G., Caldicott A. B., Goodfellow M. 1980; Thin layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 188:221–233 [CrossRef]
    [Google Scholar]
  28. 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 [CrossRef]
    [Google Scholar]
  29. 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 83:91–98 [CrossRef]
    [Google Scholar]
  30. 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 36:435–443 [CrossRef]
    [Google Scholar]
  31. Pagani H., Parenti F. 1978; Kineosporia, a new genus of the order Actinomycetales . Int J Syst Bacteriol 28:401–406 [CrossRef]
    [Google Scholar]
  32. 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 109:263–267 [CrossRef]
    [Google Scholar]
  33. Saddler G. S., Tavecchia P., Lociuro S., Zanol M., Colombo E., Selva E. 1991; Analysis of madurose and other actinomycete whole cell sugars by gas chromatography. J Microbiol Methods 14:185–191 [CrossRef]
    [Google Scholar]
  34. 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]
  35. Sakiyama Y., Thao N. K., Giang N. M., Miyadoh S., Hop D. V., Ando K. 2009; Kineosporia babensis sp. nov., isolated from plant litter in Vietnam. Int J Syst Evol Microbiol 59:550–554 [CrossRef][PubMed]
    [Google Scholar]
  36. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [CrossRef]
    [Google Scholar]
  37. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. 1997; Proposal for a new hierarchic classification system, Actinobacteria classis. nov.. Int J Syst Bacteriol 47:479–491 [CrossRef]
    [Google Scholar]
  38. Staneck J. L., Roberts G. D. 1974; Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231[PubMed]
    [Google Scholar]
  39. 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 48:995–1005 [CrossRef][PubMed]
    [Google Scholar]
  40. Tamura T., Hayakawa M., Hatano K. 1999; Sporichthya brevicatena sp. nov.. Int J Syst Bacteriol 49:1779–1784 [CrossRef][PubMed]
    [Google Scholar]
  41. Tamura T., Ishida Y., Otoguro M., Yamamura H., Hayakawa M., Suzuki K. 2010; Angustibacter luteus gen. nov., sp. nov., isolated from subarctic forest soil. Int J Syst Evol Microbiol 60:2441–2445 [CrossRef][PubMed]
    [Google Scholar]
  42. 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 54:999–1000 [CrossRef][PubMed]
    [Google Scholar]
  43. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  44. Uchida K., Aida K. 1984; An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. J Gen Appl Microbiol 30:131–134 [CrossRef]
    [Google Scholar]
  45. 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 54:253–259 [CrossRef][PubMed]
    [Google Scholar]
  46. Yokota A., Tamura T., Nishii T., Hasegawa T. 1993; Kineococcus aurantiacus gen. nov., a new aerobic, gram-positive, motile coccus with meso-diaminopimelic acid and arabinogalactan in the cell wall. Int J Syst Bacteriol 43:52–57 [CrossRef]
    [Google Scholar]
  47. 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 57:56–59 [CrossRef][PubMed]
    [Google Scholar]
  48. 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 46:519–525 [CrossRef]
    [Google Scholar]
  49. Zhang Y.-Q., Chen J., Liu H.-Y., Zhang Y.-Q., Li W.-J., Yu L.-Y. 2010; Geodermatophilus ruber sp. nov., isolated from the rhizosphere soil of a medicinal plant. Int J Syst Evol Microbiol 60:190–193
    [Google Scholar]
  50. Zhi X.-Y., Li W.-J., Stackebrandt E. 2009; 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 59:589–608 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.030007-0
Loading
/content/journal/ijsem/10.1099/ijs.0.030007-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

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