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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 5

sp. nov., a novel actinobacterium with antimicrobial activity isolated from the rhizospheric soil of D. Don No Access

Abstract

A novel actinobacterium, designated strain CWNU-1, was isolated from the rhizospheric soil of D. Don and examined using a polyphasic taxonomic approach. The organism developed pale blue aerial mycelia that was simply branched and terminated in open or closed coils of three or more volutions on International Project 3 agar. Spores were ellipsoidal to cylindrical with wrinkled surfaces. The strain showed high 16S rRNA gene sequence similarity to NBRC 13192 (98.8 %), NBRC 13354 (98.7 %) and JCM 9920 (98.6 %). The phylogenetic result based on 16S rRNA gene and genome sequences clearly demonstrated that strain CWNU-1 formed an independent phylogenetic lineage. On the basis of orthologous average nucleotide identity, CWNU-1 was most closely related to NBRC 13601 with 79.3 % identity. The results of the digital DNA–DNA hybridization analysis also indicated low levels of relatedness with other species, as the highest value was observed with NBRC 13601 (25.3 %). With reference to phenotypic characteristics, phylogenetic data, orthologous average nucleotide identity and digital DNA–DNA hybridization results, strain CWNU-1 was readily distinguished from its most closely related strains and classified as representing a novel species, for which the name sp. nov. is proposed. The type strain is CWNU-1 (=CGMCC 4.7758=MCCC 1K07402=JCM 35391).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): biosynthetic gene clusters , phylogenomic tree and polyphasic taxonomy
Funding
This study was supported by the:
  • Fundamental Research Funds of China West Normal University (Award 20A021)
    • Principle Award Recipient: XiaoJiang
  • Fundamental Research Funds of China West Normal University (Award 19B034)
    • Principle Award Recipient: ZhaoxuMa
  • Fundamental Research Funds of China West Normal University (Award 18Q044)
    • Principle Award Recipient: ZhaoxuMa
  • Natural Science Foundation of Sichuan Province (Award 2022NSFSC1661)
    • Principle Award Recipient: ZhaoxuMa
© 2024 The Authors
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References

  1. Lee JH, Kim YS, Kim SB. Streptomyces guryensis sp. nov. exhibiting antimicrobial activity, isolated from riverside soil. Int J Syst Evol Microbiol 2023; 73:5679 [View Article] [PubMed]
     [Google Scholar]
  2. Kämpfer P. Genus I. Streptomyces Waksman and Henrici 1943, 399AL emend Witt and Stackbrandt 1990, 370 emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen 1992, 159. In Whitman WB, Parte A, Goodfellow M, Kämpfer P, Busse H. eds Bergey’s Manual of Systematic Bacteriology: The Actinobacteria Part A New York: Springer; 2012 pp 1455–1781
     [Google Scholar]
  3. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. eds Actinomycete Taxonomy Arlington, VA: Society of Industrial Microbiology: Special Publication; 1980 pp 227–291
     [Google Scholar]
  4. Bérdy J. Bioactive microbial metabolites. J Antibiot 2005; 58:1–26 [View Article]
     [Google Scholar]
  5. She WQ, Sun ZF, Yi L, Zhao SM, Liang YX. Streptomyces alfalfae sp. nov. and comparisons with its closest taxa Streptomyces silaceus, Streptomyces flavofungini and Streptomyces intermedius. Int J Syst Evol Microbiol 2016; 66:44–49 [View Article] [PubMed]
     [Google Scholar]
  6. Bai L, Liu CH X, Guo L F, Piao CH Y, Li ZH L et al. Streptomyces formicae sp. nov., a novel actinomycete isolated from the head of Camponotus japonicus Mayr. Antonie van Leeuwenhoek 2016; 109:253–261 [View Article]
     [Google Scholar]
  7. Mingma R, Duangmal K, Thamchaipenet A, Trakulnaleamsai S, Matsumoto A et al. Streptomyces oryzae sp. nov., an endophytic actinomycete isolated from stems of rice plant. J Antibiot 2015; 68:368–372 [View Article]
     [Google Scholar]
  8. Xu LH, Tiang YQ, Zhang YF, Zhao LX, Jiang CH L. Streptomyces thermogriseus, a new species of the genus Streptomyces from soil, lake and hot-spring. Int J Syst Bacteriol 1998; 48:1089–1093 [View Article] [PubMed]
     [Google Scholar]
  9. Silva FSP, Souza DT, Zucchi TD, Pansa CC, Vasconcellos R L D F et al. Streptomyces atlanticus sp. nov., a novel actinomycete isolated from marine sponge Aplysina fulva (Pallas, 1766). Antonie van Leeuwenhoek 2016; 109:1467–1474 [View Article] [PubMed]
     [Google Scholar]
  10. Phongsopitanun W, Kudo T, Ohkuma M, Pittayakhajonwut P, Suwanborirux K et al. Streptomyces verrucosisporus sp. nov., isolated from marine sediments. Int J Syst Evol Microbiol 2016; 66:3607–3613 [View Article] [PubMed]
     [Google Scholar]
  11. Wang D D, Wang S, Chen X, Xu X L, Zhu J Y et al. Antitussive, expectorant and anti-inflammatory activities of four alkaloids isolated from bulbus of Fritillaria wabuensis. J Ethnopharmacol 2012; 139:189–193 [View Article] [PubMed]
     [Google Scholar]
  12. Chinese Pharmacopoeia Commission Chinese crude drug and cut crude drug. In Pharmacopoeia of the People’s Republic of China Beijing: China Medical Science Press; 2020
     [Google Scholar]
  13. Yan XY, Tong ZH Y, Yan ZJ, Luo YQ, Tang L et al. Pharmacodynamic compariason of Fritillaria Unibracteata, Fritillaria Unibracteata Var. Wabensis and Fritillaria Thunbergii cultivated. J Chin J Exp Tradit Med Formul 2012; 18:244–248
     [Google Scholar]
  14. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Evol Microbiol 1966; 16:313–340 [View Article]
     [Google Scholar]
  15. Lee YK, Kim HW, Liu CL, Lee HK. A simple method for DNA extraction from marine bacteria that produce extracellular materials. J Microbiol Methods 2003; 52:245–250 [View Article] [PubMed]
     [Google Scholar]
  16. Loqman S, Barka EA, Clément C, Ouhdouch Y. Antagonistic actinomycetes from Moroccan soil to control the grapevine gray mold. World J Microbiol Biotechnol 2009; 25:81–91 [View Article]
     [Google Scholar]
  17. Kim M, Chun J. 16S rRNA gene-based identification of bacteria and Archaea using the Eztaxon server. Methods Microbiol 2014; 41:61–74 [View Article]
     [Google Scholar]
  18. 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]
  19. 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]
  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. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  23. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  24. Richter M, Rosselló-Móra R, Glöckner F O, 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]
  25. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [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. 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]
  28. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Gordon RE, Barnett DA, Handerhan JE, Pang CH. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  31. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicas gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993; 43:805–812 [View Article]
     [Google Scholar]
  32. Smibert RM, Krieg NR. Phenotypic characterization. In In Methods for General and Molecular Bacteriology Washington, D.C: American Society for Microbiology; pp 607–654
     [Google Scholar]
  33. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. 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]
  36. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
     [Google Scholar]
  37. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. In Microbiology vol 16 Beijing: 1984 pp 176–178
     [Google Scholar]
  38. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr 1980; 188:221–233 [View Article]
     [Google Scholar]
  39. Gao R X, Liu CH X, Zhao J W, Jia F Y, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie van Leeuwenhoek 2014; 105:307–315 [View Article] [PubMed]
     [Google Scholar]
  40. Xiang W S, Liu CH X, Wang X J, Du J, Xi L J et al. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 2011; 61:1165–1169 [View Article] [PubMed]
     [Google Scholar]
  41. Hasegawa T, Yamano T, Yoneda M. Streptomyces inusitatus sp. nov. Int J Syst Bacteriol 1978; 28:407–410 [View Article]
     [Google Scholar]
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Streptomyces albipurpureus sp. nov., a novel actinobacterium with antimicrobial activity isolated from the rhizospheric soil of Fritillaria cirrhosa D. Don
Int J Syst Evol Microbiol 74, 006357 (2024); https://doi.org/10.1099/ijsem.0.006357
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