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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 5

sp. nov., a novel actinomycete with antimicrobial potential isolated from rhizosphere soil of in Guangxi No Access

Abstract

A novel strain, designated as HNM1077, was isolated from rhizosphere soil of collected from the bank of the Beilun River in Dongxing City, Guangxi Province, China. The novel strain exhibited antimicrobial activity against a wide range of microbes, particularly Gram­-negative bacteria and plant pathogenic fungi. Based on the alignment of 16S rRNA gene sequences, strain HNM1077 was closely related to NRRL B-2218 (99.51%). Comparisons based on genome sequencing showed that strain HNM1077 was distinguished from its nearest species by average nucleotide identity of 94.36% and a digital DNA–DNA hybridization value of 54.3%. The G+C content of strain HNM1077 was 73.1 mol%. The main fatty acids of strain HNM1077 were -C (21.5%), -C (11.7%), -C (8.6%), -C (9.3%) and -C (8.7%). The predominant menaquinone was MK-9 (H). The major polar lipids of strain HNM1077 consisted of phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol and glycosylphosphatidylinositol. Based on these polyphasic taxonomic results, strain HNM1077 represents a novel species, for which the name sp. nov. is proposed. The type strain is HNM1077 (=CCTCC AA 2024052=KCTC 59330).

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Keyword(s): antimicrobial potential , Hibiscus tiliaceus , Kitasatospora hibisci sp. nov. and polyphasic taxonomy
Funding
This study was supported by the:
  • Key Laboratory of Agricultural Information Service Technology (Award CATASCXTD202312)
    • Principle Award Recipient: ZhikaiGuo
  • Key Technologies Research and Development Program (Award 2022YFA1304400)
    • Principle Award Recipient: JiyangWang
  • Guangxi Natural Science Foundation of China (Award 2021GXNSFAA196044)
    • Principle Award Recipient: ShuangqingZhou
© 2025 The Authors
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2025-05-14
2025-06-18
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References

  1. Omura S, Takahashi Y, Iwai Y, Tanaka H. Kitasatosporia, a new genus of the order Actinomycetales. J Antibiot 1982; 35:1013–1019 [View Article]
     [Google Scholar]
  2. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article] [PubMed]
     [Google Scholar]
  3. Kim SB, Lonsdale J, Seong CN, 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 1943; 83:107–116
     [Google Scholar]
  4. Takahashi Y, Seino A, Iwai Y, Omura S. Taxonomic study and morphological differentiation of an actinomycete genus, Kitasatospora. Zentralbl Bakteriol 1999; 289:265–284 [View Article] [PubMed]
     [Google Scholar]
  5. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article]
     [Google Scholar]
  6. Girard G, Willemse J, Zhu H, Claessen D, Bukarasam K et al. Analysis of novel kitasatosporae reveals significant evolutionary changes in conserved developmental genes between Kitasatospora and Streptomyces. Antonie van Leeuwenhoek 2014; 106:365–380 [View Article] [PubMed]
     [Google Scholar]
  7. Takahashi Y. Genus Kitasatospora, taxonomic features and diversity of secondary metabolites. J Antibiot 2017; 70:506–513 [View Article]
     [Google Scholar]
  8. Wei Y, Wang G, Li Y, Gan M. The secondary metabolites from genus Kitasatospora: a promising source for drug discovery. Chem Biodivers 2024; 21:e202401473 [View Article] [PubMed]
     [Google Scholar]
  9. Kuester E, Williams ST. Selection of media for isolation of streptomycetes. Nature 1964; 202:928–929 [View Article] [PubMed]
     [Google Scholar]
  10. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-E: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  13. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  14. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  15. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  17. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  18. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  19. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  20. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  21. Azad SM, Jin Y, Ser HL, Goh BH, Lee LH et al. Biological insights into the piericidin family of microbial metabolites. J Appl Microbiol 2022; 132:772–784 [View Article] [PubMed]
     [Google Scholar]
  22. Shi J, Liu CL, Zhang B, Guo WJ, Zhu J et al. Genome mining and biosynthesis of kitacinnamycins as a STING activator. Chem Sci 2019; 10:4839–4846 [View Article] [PubMed]
     [Google Scholar]
  23. Murase H, Noguchi T, Sasaki S. Evaluation of simultaneous binding of chromomycin A3 to the multiple sites of DNA by the new restriction enzyme assay. Bioorg Med Chem Lett 2018; 28:1832–1835 [View Article] [PubMed]
     [Google Scholar]
  24. Igarashi Y, Futamata K, Fujita T, Sekine A, Senda H et al. Yatakemycin, a novel antifungal antibiotic produced by Streptomyces sp. TP-A0356. J Antibiot 2003; 56:107–113 [View Article]
     [Google Scholar]
  25. Libis V, Antonovsky N, Zhang M, Shang Z, Montiel D et al. Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences. Nat Commun 2019; 10:3848 [View Article] [PubMed]
     [Google Scholar]
  26. Kim J, Lee Y-J, Shin D-S, Jeon S-H, Son K-H et al. Cosmomycin C inhibits signal transducer and activator of transcription 3 (STAT3) pathways in MDA-MB-468 breast cancer cell. Bioorg Med Chem 2011; 19:7582–7589 [View Article] [PubMed]
     [Google Scholar]
  27. Shirling EBT, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  28. Kelly KL. Inter-Society Color Council–National Bureau of Standards color name charts illustrated with centroid colors. Washington, DC: US Government Printing Office; 1964
  29. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article] [PubMed]
     [Google Scholar]
  30. Lechevalier MP. The chemotaxonomy of actinomycetes. Actinomycetology 1980
     [Google Scholar]
  31. 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]
  32. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Tech Note 1990
     [Google Scholar]
  33. Bauer AW, Kirby WMM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [PubMed]
     [Google Scholar]
  34. Duda-Madej A, Stecko J, Sobieraj J, Szymańska N, Kozłowska J. Naringenin and its derivatives—health-promoting phytobiotic against resistant bacteria and fungi in humans. Antibiotics 2022; 11:1628 [View Article] [PubMed]
     [Google Scholar]
  35. Álvarez-Álvarez R, Botas A, Albillos SM, Rumbero A, Martín JF et al. Molecular genetics of naringenin biosynthesis, a typical plant secondary metabolite produced by Streptomyces clavuligerus. Microb Cell Fact 2015; 14:178 [View Article] [PubMed]
     [Google Scholar]
  36. Nishimura H, Kimura T, Tawara K, Sasaki K, Nakajima K et al. Aburamycin, a new antibiotic. J Antibiot 1957; 10:205–212
     [Google Scholar]
  37. Groth I, Schütze B, Boettcher T, Pullen CB, Rodriguez C et al. Kitasatospora putterlickiae sp. nov., isolated from rhizosphere soil, transfer of Streptomyces kifunensis to the genus Kitasatospora as Kitasatospora kifunensis comb. nov., and emended description of Streptomyces aureofaciens Duggar 1948. Int J Syst Evol Microbiol 2003; 53:2033–2040 [View Article] [PubMed]
     [Google Scholar]
  38. Kim MJ, Roh SG, Kim M-K, Park C, Kim S et al. Kitasatospora acidiphila sp. nov., isolated from pine grove soil, exhibiting antimicrobial potential. Int J Syst Evol Microbiol 2020; 70:5567–5575 [View Article] [PubMed]
     [Google Scholar]
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Kitasatospora hibisci sp. nov., a novel actinomycete with antimicrobial potential isolated from rhizosphere soil of Hibiscus tiliaceus in Guangxi
Int J Syst Evol Microbiol 75, 006787 (2025); https://doi.org/10.1099/ijsem.0.006787
/content/journal/ijsem/10.1099/ijsem.0.006787
/content/journal/ijsem/10.1099/ijsem.0.006787
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