1887

Abstract

Endophytic actinobacterial strain 3R004 was isolated from a root of collected in Thailand. In this report, the taxonomic position of this strain is described using a polyphasic approach. Based on the morphological characteristics and chemical composition of its cells, strain 3R004 was identified as a member of the genus . It produced a long chain of cylindrical spores on aerial mycelia. -Diaminopimelic acid was detected in the cell wall peptidoglycan. The menaquinones were MK-9(H), MK-9(H) and MK-9(H). C, iso-C, anteiso-C and iso-C were detected as the major cellular fatty acids. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and one unidentified lipid. Strain 3R004 showed the highest 16S rRNA gene similarity of 99.45 % to MK-45. The phylogenomic results indicated that strain 3R004 was close to GGCR-6 and DSM 40234. The DNA–DNA hybridization and average nucleotide identity values among strain 3R004 and closely related species were 35.5–63.1 % and 82.7–94.3 %, respectively. The type strain produced actinomycin D antibiotic as the major secondary metabolite. The maximum productivity of the actinomycin D (378 mg l) was observed when the strain was grown in 301 broth at 30 °C, 180 r.p.m. for 12 days. On the basis of phenotypic and genotypic evidence, strain 3R004 represents a novel species of the genus , for which the name is proposed. The type strain is 3R004 (=LMG 32138=TBRC 13128=NBRC 115065).

Funding
This study was supported by the:
  • Ratchadaphiseksomphot Endowment Fund; Chulalongkorn University (Award DNS 63_079_33_005_1)
    • Principle Award Recipient: WongsakornPhongsopitanun
  • Thailand Research Fund (Award MRG6180011)
    • Principle Award Recipient: WongsakornPhongsopitanun
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005017
2021-09-22
2021-10-24
Loading full text...

Full text loading...

References

  1. Bérdy J. Bioactive microbial metabolites. J Antibiot 2005; 58:1–26 [View Article]
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  3. Yan X, Li Y, Wang N, Chen Y, Huang L-L. Streptomyces ginkgonis sp. nov., an endophyte from Ginkgo biloba. Antonie van Leeuwenhoek 2018; 111:891–896 [View Article] [PubMed]
    [Google Scholar]
  4. Wang Z, Jiang B, Li X, Gan L, Long X et al. Streptomyces populi sp. nov., a novel endophytic actinobacterium isolated from stem of Populus adenopoda Maxim. Int J Syst Evol Microbiol 2018; 68:2568–2573 [View Article] [PubMed]
    [Google Scholar]
  5. Wang H-F, Li Q-L, Xiao M, Zhang Y-G, Zhou X-K et al. Streptomyces capparidis sp. nov., a novel endophytic actinobacterium isolated from fruits of Capparis spinosa L. Int J Syst Evol Microbiol 2017; 67:133–137 [View Article] [PubMed]
    [Google Scholar]
  6. Phongsopitanun W, Sripreechasak P, Rueangsawang K, Panyawut R, Pittayakhajonwut P et al. Diversity and antimicrobial activity of culturable endophytic actinobacteria associated with Acanthaceae plants. ScienceAsia 2020; 46:288 [View Article]
    [Google Scholar]
  7. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  8. 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]
  9. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975
    [Google Scholar]
  10. Williams ST, Cross T. Chapter XI actinomycetes. Methods Microbiol 1971; 4:295–334
    [Google Scholar]
  11. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  12. 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 [View Article]
    [Google Scholar]
  13. Uchida K, Aida KO. An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. J Gen Appl Microbiol 1984; 30:131–134 [View Article]
    [Google Scholar]
  14. 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 [View Article]
    [Google Scholar]
  15. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  16. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–148
    [Google Scholar]
  17. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  19. Felsenstein J. Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 1983; 14:313–333 [View Article]
    [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  21. Jukes TH, Cantor CR. Evolution of protein molecules. Munro H. eds In Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  22. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  24. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  25. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [View Article] [PubMed]
    [Google Scholar]
  26. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  27. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  28. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–46 [View Article] [PubMed]
    [Google Scholar]
  29. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  30. Lechevalier MP, De Bievre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
    [Google Scholar]
  31. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kadler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on the reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  33. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  34. Tang X, Zhao J, Li K, Chen Z, Sun Y et al. Streptomyces cyaneochromogenes sp. nov., a blue pigment-producing actinomycete from manganese-contaminated soil. Int J Syst Evol Microbiol 2019; 69:2202–2207 [View Article] [PubMed]
    [Google Scholar]
  35. Zhang X, Ye X, Chai W, Lian X-Y, Zhang Z. New metabolites and bioactive actinomycins from marine-derived Streptomyces sp. ZZ338. Mar Drugs 2016; 14:181 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005017
Loading
/content/journal/ijsem/10.1099/ijsem.0.005017
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