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Streptomyces acidicola sp. nov., isolated from a peat swamp forest in Thailand

Abstract

A novel actinobacterium, designated strain K1PN6T, was isolated from soil sample collected in Kantulee peat swamp forest, Surat Thani province, Thailand. The morphological, chemotaxonomic, and phylogenetic characteristics were consistent with its classification in the genus Streptomyces. Based on 16S rRNA gene sequence analysis, strain K1PN6T showed highest similarity to Streptomyces phyllanthi PA1-07T (98.6 %), Streptomyces spongiae Sp080513SC-24T (98.3%) and Streptomyces adustus WH-9T (98.3%). The G + C content of the genomic DNA was 70.3 mol%. Digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain K1PN6T with S. phyllanthi TISTR 2346T (33.7 and 89.1%), S. spongiae NBRC 106415T (38.6 and 90.6%) and S. adustus NBRC 109810T (26.0 and 86.2%) were below the thresholds of 70 and 95–96% for prokaryotic conspecific assignation. Chemotaxonomic data revealed that strain K1PN6T possessed MK-9(H8) (45%) and MK-9(H6) (34%) as the predominant menaquinones. It contained ll-diaminopimelic acid as the diagnostic diamino acid and galactose, glucose, mannose, and ribose as whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified aminolipids, an unidentified phospholipid, and glycophospholipid. The predominant cellular fatty acids (>10%) were iso-C16:0, C16:0, anteiso-C15:0, and iso-C14:0. On the basis of these genotypic and phenotypic data, strain K1PN6T should be designated as a representative of a novel species of the genus Streptomyces, for which the name Streptomyces acidicola sp. nov. is proposed with the type strain K1PN6T (=TBRC 11341T=NBRC 114304T).

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References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol. 1943;46:337.

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Kämpfer P. Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo M, Suzuki K, et al., editors. Bergey’s manual® of systematic bacteriology. New York: Springer; 2012. p. 1679–80.

  3. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol. 1987;65:501–9.

    CAS  Google Scholar 

  4. Shirling ET, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol. 1966;16:313–40.

    Google Scholar 

  5. Jacobson E, Grauville WC, Fogs CE. Color harmony manual. 4th ed. Chicago: Container Corporation of America; 1958.

  6. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol. 1974;24:54–63.

    Google Scholar 

  7. Williams S, Goodfellow M, Alderson G, Wellington E, Sneath P, et al. Numerical classification of Streptomyces and related genera. Microbiology. 1983;129:1743–813.

    CAS  Google Scholar 

  8. Küster E, Williams S. Selection of media for isolation of streptomycetes. Nature. 1964;202:928–9.

    Google Scholar 

  9. Becker B, Lechevalier M, Lechevalier H. Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. Appl Microbiol. 1965;13:236–43.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol. 1983;29:319–22.

    CAS  Google Scholar 

  11. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol. 1974;28:226–31.

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides. J Bacteriol. 1982;151:828–37.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Minnikin D, Patel P, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Evol Microbiol. 1977;27:104–17.

    CAS  Google Scholar 

  14. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Newark, Delaware, United States: MIDI, Inc; 2001. p. 1–7.

    Google Scholar 

  15. Kieser T, Bibb M, Buttner M, Chater K, Hopwood D. Practical Streptomyces genetics. Norwich, UK: John Innes Foundation; 2000.

    Google Scholar 

  16. Mingma R, Pathom-aree W, Trakulnaleamsai S, Thamchaipenet A, Duangmal K. Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine. World J Microbiol Biotechnol. 2014;30:271–80.

    CAS  PubMed  Google Scholar 

  17. Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, et al. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 2013;41:W29–33.

    PubMed  PubMed Central  Google Scholar 

  18. 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;67:1613–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol. 1971;20:406–16.

    Google Scholar 

  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–76.

    CAS  PubMed  Google Scholar 

  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.

    CAS  PubMed  Google Scholar 

  22. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.

    PubMed  Google Scholar 

  24. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–5.

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinforma. 2013;14:60.

    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;32:929–31.

    CAS  PubMed  Google Scholar 

  28. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 2019;47:W81–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Lechevalier MP, De Bievre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol. 1977;5:249–60.

    CAS  Google Scholar 

  30. Kim SB, Lonsdale J, Seong C-N, Goodfellow M. Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943) AL) emend. Rainey et al. 1997. Antonie van Leeuwenhoek. 2003;83:107–16.

    CAS  PubMed  Google Scholar 

  31. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol. 2018;68:461–6.

    CAS  PubMed  Google Scholar 

  32. Klykleung N, Phongsopitanun W, Pittayakhajonwut P, Ohkuma M, Kudo T, et al. Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus. Int J Syst Evol Microbiol. 2016;66:3923–8.

    CAS  PubMed  Google Scholar 

  33. Khan ST, Komaki H, Motohashi K, Kozone I, Mukai A, et al. Streptomyces associated with a marine sponge Haliclona sp.; Biosynthetic genes for secondary metabolites and products. Evol Microbiol. 2011;13:391–403.

    CAS  Google Scholar 

  34. Lee H-J, Whang K-S. Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil. Int J Syst Bacteriol. 2016;66:3573–8.

    CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by Center of Excellence on Biodiversity (BDC), Office of Higher Education Commission (Project Code BDC-PG1-160003) and a research grant No.T-2.2 (Prog.)13.62 from Kasetsart University Research and Development Institute (KURDI). The authors are grateful to the government agency in Kantulee, Surat Thani province, Thailand for sample collection.

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Lipun, K., Chantavorakit, T., Mingma, R. et al. Streptomyces acidicola sp. nov., isolated from a peat swamp forest in Thailand. J Antibiot 73, 435–440 (2020). https://doi.org/10.1038/s41429-020-0294-5

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