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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 3

sp. nov., isolated from mountain forest soil No Access

Abstract

A novel actinomycete, strain SMC 257, was isolated from a soil sample collected from mountain forest, Nan Province, Thailand. Strain SMC 257 formed tightly closed spiral spore chains on aerial mycelia. A polyphasic approach was used for the taxonomic study of this strain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 257 belonged to the genus , and the closest phylogenetically related species were subsp. JCM 9946 (98.9 % 16S rRNA gene sequence similarity), TBRC 6557 (98.4 %), and subsp. JCM 3145 (98.3 %). Genome sequencing revealed a genome size of 9.76 Mbp and a G+C content of 72.3 mol%. The genome average nucleotide identity (ANI) and the digital DNA–DNA hybridization (dDDH) values that distinguished this novel strain from its closest related species were species boundary of 95–96 % and 70 %, respectively. The cell wall peptidoglycan contained -diaminopimelic acid. The whole-cell sugars were glucose, ribose, madurose and mannose. The major menaquinone was MK-9(H). The polar lipid profile consisted of phosphatidylethanolamine, hydroxyphosphatidylethanolamine, lysophosphatidylethanolamine, diphosphatidylglycerol, N-phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The predominant cellular fatty acids were C 10-methyl and iso-C. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, strain SMC 257 is considered to represent a novel species of the genus , for which the name is proposed. The type strain is SMC 257 (=TBRC 13065=NBRC 114772).

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  • Accepted:
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Keyword(s): actinomycete , mountain forest , Nonomuraea , Streptosporangiaceae and taxonomy
Funding
This study was supported by the:
  • Mahidol University
    • Principle Award Recipient: ManeeChanama
© 2021 The Authors
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2021-02-17
2023-04-02
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References

  1. Zhang Z, Wang Y, Ruan J. Reclassification of Thermomonospora and Microtetraspora . Int J Syst Bacteriol 1998; 48:411–422 [View Article][PubMed]
     [Google Scholar]
  2. Chiba S, Suzuki M, Ando K. Taxonomic re-evaluation of 'Nocardiopsis' sp. K-252T (= NRRL 15532T): a proposal to transfer this strain to the genus Nonomuraea as Nonomuraea longicatena sp. nov. Int J Syst Bacteriol 1999; 49 Pt 4:1623–1630 [View Article][PubMed]
     [Google Scholar]
  3. Kämpler P et al. Genus VI. Nonomuraea . In Goodfellow M, Kämpler P, Busse H-J, Trujillo M, Suzuki K-I. (editors) Bergey’s Manual of Systematic bacteriology, vol.5. The Actinobacteria, 2nd ed. New York: Springer; 2012 pp 1844–1861
     [Google Scholar]
  4. Sripreechasak P, Phongsopitanun W, Supong K, Pittayakhajonwut P, Kudo T et al. Nonomuraea rhodomycinica sp. nov., isolated from peat swamp forest soil. Int J Syst Evol Microbiol 2017; 67:1683–1687 [View Article][PubMed]
     [Google Scholar]
  5. Xi L, Zhang L, Ruan J, Huang Y. Nonomuraea martima sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2011; 61:2740–2744 [View Article][PubMed]
     [Google Scholar]
  6. Lipun K, Teo WFA, Suksaard P, Pathom-Aree W, Duangmal K. Nonomuraea antri sp. nov., an actinomycete isolated from cave soil in Thailand. Int J Syst Evol Microbiol 2020; 70:5296–5303 [View Article][PubMed]
     [Google Scholar]
  7. Ou Y, Sheng Y, Hu X, Leng D, Huang J et al. Nonomuraea nitratireducens sp. nov., a new actinobacterium isolated from Suaeda australis Moq. rhizosphere. Int J Syst Evol Microbiol 2020; 70:5026–5031 [View Article][PubMed]
     [Google Scholar]
  8. Niemhom N, Chutrakul C, Suriyachadkun C, Thawai C. Nonomuraea stahlianthi sp. nov., an endophytic actinomycete isolated from the stem of Stahlianthus campanulatus . Int J Syst Evol Microbiol 2017; 67:2879–2884 [View Article][PubMed]
     [Google Scholar]
  9. Suzuki S, Okuda T, Komatsubara S. Selective isolation and study on the global distribution of the genus Planobispora in soils. Can J Microbiol 2001; 47:979–986 [View Article][PubMed]
     [Google Scholar]
  10. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  11. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article][PubMed]
     [Google Scholar]
  12. Monciardini P, Sosio M, Cavaletti L, Chiocchini C, Donadio S. New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol Ecol 2002; 42:419–429 [View Article][PubMed]
     [Google Scholar]
  13. Hall TA. BioEdit: a user friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  14. 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]
  15. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
     [Google Scholar]
  17. 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]
  18. Felsenstein J. Parsimony in systematic: biological and statistical issues. Annu Rev Ecol Syst 1983; 14:313–333 [View Article]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  21. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. 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]
  24. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
     [Google Scholar]
  25. 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; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  26. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  27. Kelly KL. Inter-Society Color Council - National Bureau of Standard Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  28. Itoh T, Kudo T, Parenti F, Seino A. Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Syst Bacteriol 1989; 39:168–173 [View Article]
     [Google Scholar]
  29. 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 [View Article]
     [Google Scholar]
  30. Arai T. Culture Media for Actinomycetes Tokyo: Japanese Society for Actinomycetes; 1975
     [Google Scholar]
  31. Williams ST, Cross T. Actinomycetes. Methods Microbiol 1971; 4:295–334
     [Google Scholar]
  32. Tamura T, Nakagaito Y, Nishii T, Hasegawa T, Stackebrandt E et al. A new genus of the order Actinomycetales, Couchioplanes gen. nov., with descriptions of Couchioplanes caeruleus (Horan and Brodsky 1986) comb. nov. and Couchioplanes caeruleus subsp. azureus subsp. nov. Int J Syst Bacteriol 1994; 44:193–203 [View Article][PubMed]
     [Google Scholar]
  33. 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]
  34. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  35. Minnikin DE, 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]
  36. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, Technical Note#. 2001
     [Google Scholar]
  37. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  38. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16:176–178
     [Google Scholar]
  39. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
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Nonomuraea montanisoli sp. nov., isolated from mountain forest soil
Int J Syst Evol Microbiol 71, 004695 (2021); https://doi.org/10.1099/ijsem.0.004695
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