1887

Abstract

A novel Gram-stain-positive strain with sandy aerial mycelium and golden yellow substrate mycelium, designated fd2-tb, was isolated from a soil sample collected in Shanghai, China, and its taxonomic status was established by phylogenetic analysis. 16S rRNA gene sequence analysis showed that strain fd2-tb belonged to the genus and was related to JCM 19660 (99.9 % 16S rRNA gene sequence similarity), NBRC 12770 (99.9 %), NBRC 13072 (99.8 %), NRRL B-5430 (99.7 %), LMG 19896 (99.5 %), NBRC 12823 (99.5 %) and NBRC 13447 (99.3 %). The cell wall of strain fd2-tb contained -diaminopimelic acid, and whole-cell sugars were identified as glucose and ribose. The menaquinones MK-9(H), MK-9(H) and MK-9(H) were also detected. In addition, the polar lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, as well as five unidentified phospholipids, were detected. Major cellular fatty acids were identified as anteiso-C, iso-C, anteiso-C, iso-C and C. DNA–DNA hybridization experiments showed that strain fd2-tb exhibited 36.5 ± 0.6 %, 43.5 ± 2.0 %, 11.1 ± 1.3 %, 10.3 ± 3.1 %, 9.8 ± 1.9 %, 48.9 ± 3.9 % and 16.3 ± 1.7 % relatedness to JCM 40119660, NBRC 12770, NBRC 13072, NRRL B-5430, LMG 19896, NBRC 12823 and NBRC 13447, respectively. Based on these analyses as well as some phenotypic differences, strain fd2-tb is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is fd2-tb ( = DSM 100336 = CGMCC 4.7256).

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2016-03-01
2020-01-24
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References

  1. Collins M. D.. 1985; Isoprenoid quinone analysis in classification and identification. In Chemical Methods in Bacterial Systematics pp267–287Edited by Goodfellow M., Minnikin D. E.. London: Academic Press;
    [Google Scholar]
  2. De Ley J., Cattoir H., Reynaerts A.. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  3. Edgar R. C.. 2004; muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  4. Felsenstein J.. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  5. Felsenstein J.. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution39:783–791 [CrossRef]
    [Google Scholar]
  6. Gause G. F., Preobrazhenskaya T. P., Sveshnikova M. A., Terekhova L. P., Maximova T. S.. 1983; A Guide for the Determination of Actinomycetes Moscow: Nauka;
    [Google Scholar]
  7. Goodfellow M., Fiedler H. P.. 2010; A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie van Leeuwenhoek98:119–142 [CrossRef][PubMed]
    [Google Scholar]
  8. Huss V. A., Festl H., Schleifer K. H.. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol4:184–192 [CrossRef][PubMed]
    [Google Scholar]
  9. Jones K. L.. 1949; Fresh isolates of Actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol57:141–145[PubMed]
    [Google Scholar]
  10. Kämpfer P.. 2012a; Family I. Streptomycetaceae Waksman and Herrici 1943, 339AL emend. Rainey, Ward-Rainey and Stackebrandt 1997, 486 emend. Kim, Lonsdale, Seong and Goodfellow 2003b, 113 emend Zhi, Li and Stackebrandt 2009, 600. In Bergey's Manual of Systematic Bacteriology vol. 5 The Actinobacteria, Part B, 2nd edn. pp1446–1454Edited by Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M. E., Suzuki K., Ludwig W., Whitman W. B.. New York: Springer;[CrossRef]
    [Google Scholar]
  11. Kämpfer P.. 2012b; Genus I. Streptomyces Waksman and Henrici 1943, 339 emend. Witt and Stackebrandt 1990, 370 emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen 1992, 159. In Bergey's Manual of Systematic Bacteriology vol. 5 The Actinobacteria, Part B, 2nd edn. pp1455–1767Edited by Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M. E., Suzuki K., Ludwig W., Whitman W. B.. New York: Springer;[CrossRef]
    [Google Scholar]
  12. Kelly K. L.. 1964; Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office;
    [Google Scholar]
  13. Kim S. B., Falconer C., Williams E., Goodfellow M.. 1998; Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int J Syst Bacteriol48:59–68 [CrossRef][PubMed]
    [Google Scholar]
  14. Kim S. B., Lonsdale J., Seong C. N., Goodfellow M.. 2003; Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943)AL) emend. Rainey. 1997. Antonie van Leeuwenhoek83:107–116 [CrossRef][PubMed]
    [Google Scholar]
  15. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., other authors. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  16. Kluge A. G., Farris J. S.. 1969; Quantitative phyletics and evolution of anurans. Syst Zool18:1–32 [CrossRef]
    [Google Scholar]
  17. 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 Seriesvol 20 pp173–199Edited by Goodfellow M., Minnikin D. E.. New York: Academic Press;
    [Google Scholar]
  18. Labeda D. P., Goodfellow M., Brown R., Ward A. C., Lanoot B., Vanncanneyt M., Swings J., Kim S. B., Liu Z., other authors. 2012; Phylogenetic study of the species within the family Streptomycetaceae . Antonie van Leeuwenhoek101:73–104 [CrossRef][PubMed]
    [Google Scholar]
  19. Lane D. J.. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp115–175Edited by Stackebrandt E., Goodfellow M.. New York: Wiley;
    [Google Scholar]
  20. Lechevalier M. P., Lechevalier H. A.. 1970; Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol20:435–443 [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 Methods2:233–241 [CrossRef]
    [Google Scholar]
  22. Munoz R., Yarza P., Ludwig W., Euzéby J., Amann R., Schleifer K. H., Glöckner F. O., Rosselló-Móra R.. 2011; Release LTPs104 of the all-species living tree. Syst Appl Microbiol34:169–170 [CrossRef][PubMed]
    [Google Scholar]
  23. Parte A. C.. 2014; LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res42:(D1)D613–D616 [CrossRef][PubMed]
    [Google Scholar]
  24. Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J., Glöckner F. O.. 2013; The silva ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res41:(D1)D590–D596 [CrossRef][PubMed]
    [Google Scholar]
  25. Rzhetsky A., Nei M.. 1992; A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol9:945–967
    [Google Scholar]
  26. Saitou N., Nei M.. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4:406–425[PubMed]
    [Google Scholar]
  27. Sasser M.. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl20:16
    [Google Scholar]
  28. Shima J., Penyige A., Ochi K.. 1996; Changes in patterns of ADP-ribosylated proteins during differentiation of Streptomyces coelicolor A3(2) and its development mutants. J Bacteriol178:3785–3790[PubMed]
    [Google Scholar]
  29. Shirling E. B., Gottlieb D.. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol16:313–340 [CrossRef]
    [Google Scholar]
  30. Staneck J. L., Roberts G. D.. 1974; Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol28:226–231[PubMed]
    [Google Scholar]
  31. 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 Evol28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  32. Turner S., Pryer K. M., Miao V. P. W., Palmer J. D.. 1999; Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol46:327–338 [CrossRef][PubMed]
    [Google Scholar]
  33. Waksman S. A., Henrici A. T.. 1943; The nomenclature and classification of the actinomycetes. J Bacteriol46:337–341[PubMed]
    [Google Scholar]
  34. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. 1987; International Committee on Bacterial Systematics. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol37:463–464 [CrossRef]
    [Google Scholar]
  35. Williams S. T., Goodfellow M., Alderson G., Wellington E. M., Sneath P. H., Sackin M. J.. 1983; Numerical classification of Streptomyces and related genera. J Gen Microbiol129:1743–1813[PubMed]
    [Google Scholar]
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