1887

Abstract

A novel aerobic actinomycete, designated strain I12A-02601, was isolated from a desert soil crusts sample collected from the Shapotou region of Tengger Desert, north-west China. The substrate mycelia of this isolate were well-developed and branched, but not fragmented. The maturity aerial mycelia formed short chains of small, rod-shaped spores. The strain contained -diaminopimelic acid, -diaminopimelic acid, galactose, glucose, ribose and xylose in its whole-cell hydrolysates. The polar lipids consisted of diphosphatidylglycerol, -acetylglucosamine-containing phospholipids, phosphatidylinositolmannoside and glycolipids. The predominant menaquinones were MK-10(H) and MK-10(H). The major fatty acids were iso-C, anteiso-C, C, anteiso-C and iso-C. The G+C content of the genomic DNA was 72.2 mol%. The 16S rRNA gene sequences comparison showed that strain I12A-02601 was most closely related to members of the family , such as YIM 48868 (93.3 % sequence similarity), PIP 143 (93.2 %), and EUM 378 (93.2 %). In the phylogenetic tree based on 16S rRNA gene sequences, strain I12A-02601 formed a clade with the members of the genera , , and in the family . Combined data from this taxonomic study using a polyphasic approach, led to the conclusion that strain I12A-02601 represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of the type species is I12A-02601 ( = CPCC 203544 = DSM 45829 = NBRC 109454).

Funding
This study was supported by the:
  • National Infrastructure of Microbial Resources (Award NIMR-2014-3)
  • National Natural Science Foundation of China (NSFC) (Award 81173026)
  • National S&T Major Special Project on Major New Drug Innovation (Award 2012ZX09301002-003)
  • 863 Program (Award 2014AA021504)
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2015-10-01
2024-03-28
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References

  1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. ( 1997;). Gapped blast psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25 33893402 [View Article] [PubMed].
    [Google Scholar]
  2. Cao Y.-R., Jiang Y., Wu J.Y., Xu L.-H., Jiang C.-L. ( 2009;). Actinopolymorpha alba sp. nov., isolated from a rhizosphere soil. Int J Syst Evol Microbiol 59 22002203 [View Article] [PubMed].
    [Google Scholar]
  3. Collins M.D., Pirouz T., Goodfellow M., Minnikin D.E. ( 1977;). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100 221230 [View Article] [PubMed].
    [Google Scholar]
  4. Collins M.D., Dorsch M., Stackebrandt E. ( 1989;). Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov. Int J Syst Bacteriol 39 16 [View Article].
    [Google Scholar]
  5. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376. [CrossRef]
    [Google Scholar]
  6. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783791 [View Article].
    [Google Scholar]
  7. Groth I., Schumann P., Rainey F.A., Martin K., Schuetze B., Augsten K. ( 1997;). Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 47 11291133 [View Article] [PubMed].
    [Google Scholar]
  8. Kaewkla O., Franco C.M.M. ( 2011;). Flindersiella endophytica gen. nov., sp. nov., an endophytic actinobacterium isolated from the root of Grey Box, an endemic eucalyptus tree. Int J Syst Evol Microbiol 61 21352140 [View Article] [PubMed].
    [Google Scholar]
  9. 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]
    [Google Scholar]
  10. Kimura M. ( 1983). The Neutral Theory of Molecular Evolution, pp. 263 Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  11. Kluge A.G., Farris J.S. ( 1969;). Quantitative phyletics and the evolution of anurans. Syst Zool 18 132 [View Article].
    [Google Scholar]
  12. Kovács N. ( 1956;). Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178 703 [View Article] [PubMed].
    [Google Scholar]
  13. 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. 173199. Edited by Goodfellow M., Minnikin D. E. New York: Academic Press;.
    [Google Scholar]
  14. Lechevalier H., Lechevalier M.P. ( 1965;). [Classification of aerobic actinomycetes based on their morphology and their chemical composition]. Ann Inst Pasteur (Paris) 108 662673 (in French) [PubMed].
    [Google Scholar]
  15. Lechevalier M.P., Lechevalier H.A. ( 1980;). The chemotaxonomy of actinomycetes. . In Actinomycete Taxonomy (Special Publication no. 6), pp. 227291. Edited by Dietz A., Thayer J. Arlington, VA: Society for Industrial Microbiology;.
    [Google Scholar]
  16. Lee L.H., Zainal N., Azman A.S., Mutalib N.S.A., Hong K., Chan K.G. ( 2014;). Mumia flava gen. nov., sp. nov., an actinobacterium of the family Nocardioidaceae . Int J Syst Evol Microbiol 64 14611467. [CrossRef]
    [Google Scholar]
  17. MacFaddin J.F. ( 1980). Biochemical Tests for Identification of Medical Bacteria , 2nd edn. Baltimore: Williams & Wilkins;.
    [Google Scholar]
  18. Marmur J., Doty P. ( 1962;). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5 109118 [View Article] [PubMed].
    [Google Scholar]
  19. Meier A., Kirschner P., Schröder K.H., Wolters J., Kroppenstedt R.M., Böttger E.C. ( 1993;). Mycobacterium intermedium sp. nov. Int J Syst Bacteriol 43 204209. [CrossRef]
    [Google Scholar]
  20. Miller E.S., Woese C.R., Brenner S. ( 1991;). Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov. Int J Syst Bacteriol 41 363368. [CrossRef]
    [Google Scholar]
  21. 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 [View Article].
    [Google Scholar]
  22. Nesterenko O.A., Kvasnikov E.I., Nogina T.M. ( 1985;). Nocardioidaceae fam. nov., a new family of the order Actinomycetales Buchanan 1917. Mikrobiol Zhurnal 47 312.
    [Google Scholar]
  23. Park Y.H., Yoon J.H., Shin Y.K., Suzuki K., Kudo T., Seino A., Kim H.J., Lee J.S., Lee S.T. ( 1999;). Classification of ‘Nocardioides fulvus’ IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 49 743752 [View Article] [PubMed].
    [Google Scholar]
  24. Prauser H. ( 1976;). Nocardioides, a new genus of the order Actinomycetales . Int J Syst Bacteriol 26 5865 [View Article].
    [Google Scholar]
  25. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425 [PubMed].
    [Google Scholar]
  26. Shirling E.B., Gottlieb D. ( 1966;). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16 313340 [View Article].
    [Google Scholar]
  27. Suzuki K., Komagata K. ( 1983;). Pimelobacter gen. nov., a new genus of coryneform bacteria with ll-diaminopimelic acid in the cell wall. J Gen Appl Microbiol 29 5971 [View Article].
    [Google Scholar]
  28. 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 [View Article] [PubMed].
    [Google Scholar]
  29. 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 48764882 [View Article] [PubMed].
    [Google Scholar]
  30. Urzì C., Salamone P., Schumann P., Stackebrandt E. ( 2000;). Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50 529536 [View Article] [PubMed].
    [Google Scholar]
  31. Wang Y.-M., Zhang Z.-S., Xu X.-L., Ruan J.-S., Wang Y. ( 2001;). Actinopolymorpha singaporensis gen. nov., sp. nov., a novel actinomycete from the tropical rainforest of Singapore. Int J Syst Evol Microbiol 51 467473 [PubMed]. [CrossRef]
    [Google Scholar]
  32. Wang Y.-X., Zhang Y.-Q., Xu L.-H., Li W.-J. ( 2008;). Actinopolymorpha rutila sp. nov., isolated from a forest soil. Int J Syst Evol Microbiol 58 24432446 [View Article] [PubMed].
    [Google Scholar]
  33. Xu P., Li W.-J., Xu L.-H., Jiang C.-L. ( 2003;). A microwave-based method for genomic DNA extraction from actinomycetes. Microbiology [English translation of Microbiology (Beijing)] 30 8284.
    [Google Scholar]
  34. Yabe S., Aiba Y., Sakai Y., Hazaka M., Yokota A. ( 2011;). Thermasporomyces composti gen. nov., sp. nov., a thermophilic actinomycete isolated from compost. Int J Syst Evol Microbiol 61 8690 [View Article] [PubMed].
    [Google Scholar]
  35. Yuan L.-J., Zhang Y.-Q., Yu L.-Y., Sun C.-H., Wei Y.-Z., Liu H.-Y., Li W.-J., Zhang Y.-Q. ( 2010;). Actinopolymorpha cephalotaxi sp. nov., a novel actinomycete isolated from rhizosphere soil of the plant Cephalotaxus fortunei . Int J Syst Evol Microbiol 60 5154 [View Article] [PubMed].
    [Google Scholar]
  36. 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 589608 [PubMed]. [CrossRef]
    [Google Scholar]
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