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

Volume 75, Issue 1

sp. nov., sp. nov. and sp. nov. isolated from a cave, and an emended description of the genus No Access

Abstract

Six Gram-reaction-positive, strictly aerobic, mycelium-forming actinobacteria were isolated from soils collected from a natural cave in Jeju, Republic of Korea. The isolates produced well-developed, branched, substrate mycelia and white aerial mycelia that differentiated into straight or flexuous chains of smooth-surfaced spores. Cells showed growth at 15–30 °C, pH 3.5–8.0 and 0–1% (w/v) NaCl. Most of the isolates also grew at pH 10.0. The cell-wall peptidoglycan in common contained -diaminopimelic acid, galactose, glucose, mannose and rhamnose. The major menaquinone was MK-9(H) and MK-9(H). The polar lipids in common contained phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid, with the presence of diphosphatidylglycerol and phosphatidylethanolamine in some strains. The predominant fatty acids in common were anteiso-C, iso-C and C. Strains N1-1, N1-3 and N1-12 contained genomes of 8.44–8.77 Mbp, and strains N1-5 and N1-10 consisted of genomes of 9.00–9.17 Mbp, while strain N8-3 contained the smallest genome (7.33 Mbp) among the isolates. The genomic DNA G+C contents of the isolates were 71.5–72.2%. Three representatives of the isolates encompassed 16–29 biosynthetic gene clusters predicted to encode for secondary metabolites. The core genome-based phylogenomic tree showed that they formed three distinct clusters within the genus s, with the closest relative, the type strain of s , which was also supported by 16S rRNA gene phylogeny. The orthologous average nucleotide identity (≤88.2%) and digital DNA–DNA hybridization (≤30.3%) between three representatives of the isolates and members of the genus s and among them supported that the isolates represent three new species of the genus s, for which the names [type strain, N1-1 (=KCTC 19224=DSM 45080)], [type strain, N8-3 (=KCTC 29470=DSM 117389)] and sp. nov. [type strain, N1-10 (=KCTC 19257=DSM 117391=NRRL B-24556)] are proposed.

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Keyword(s): cave , genus Streptacidiphilus , Streptacidiphilus alkalitolerans sp. nov. , Streptacidiphilus cavernicola sp. nov. and Streptacidiphilus jeojiensis sp. nov.
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2025-01-31
2025-11-12

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References

  1. 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 1997; 83:107–116
     [Google Scholar]
  2. Euzeby JP. Validation list no.93. list of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2003; 53:1219–1220 [View Article]
     [Google Scholar]
  3. Nouioui I, Klenk HP, Igual JM, Gulvik CA, Lasker BA et al. Streptacidiphilus bronchialis sp. nov., a ciprofloxacin-resistant bacterium from a human clinical specimen; reclassification of Streptomyces griseoplanus as Streptacidiphilus griseoplanus comb. nov. and emended description of the genus Streptacidiphilus. Int J Syst Evol Microbiol 2019; 69:1047–1056 [View Article] [PubMed]
     [Google Scholar]
  4. Wang L, Huang Y, Liu Z, Goodfellow M, Rodríguez C. Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand. Int J Syst Evol Microbiol 2006; 56:1257–1261 [View Article] [PubMed]
     [Google Scholar]
  5. Madhaiyan M, Saravanan VS, See-Too W-S, Volpiano CG, Sant’Anna FH et al. Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera. Int J Syst Evol Microbiol 2022; 72:5570 [View Article] [PubMed]
     [Google Scholar]
  6. Huang Y, Cui Q, Wang L, Rodriguez C, Quintana E et al. Streptacidiphilus jiangxiensis sp. nov., a novel actinomycete isolated from acidic rhizosphere soil in China. Antonie van Leeuwenhoek 2004; 86:159–165 [View Article] [PubMed]
     [Google Scholar]
  7. Song W, Duan L, Jin L, Zhao J, Jiang S et al. Streptacidiphilus monticola sp. nov., a novel actinomycete isolated from soil. Int J Syst Evol Microbiol 2018; 68:1757–1761 [View Article] [PubMed]
     [Google Scholar]
  8. Yu B, Han C, Zhao J, Zhang Y, Shan Q et al. Streptacidiphilus fuscans sp. nov., a novel actinobacterium isolated from the root of pumpkin (Cucurbita moschata). Int J Syst Evol Microbiol 2021; 71:4824 [View Article]
     [Google Scholar]
  9. Cho SH, Han JH, Ko HY, Kim SB. Streptacidiphilus anmyonensis sp. nov., Streptacidiphilus rugosus sp. nov. and Streptacidiphilus melanogenes sp. nov., acidophilic actinobacteria isolated from Pinus soils. Int J Syst Evol Microbiol 2008; 58:1566–1570 [View Article] [PubMed]
     [Google Scholar]
  10. Golinska P, Dahm H, Goodfellow M. Streptacidiphilus toruniensis sp. nov., isolated from a pine forest soil. Antonie van Leeuwenhoek 2016; 109:1583–1591 [View Article] [PubMed]
     [Google Scholar]
  11. Roh SG, Kim MK, Park S, Yun BR, Park J et al. Streptacidiphilus pinicola sp. nov., isolated from pine grove soil. Int J Syst Evol Microbiol 2018; 68:3149–3155 [View Article] [PubMed]
     [Google Scholar]
  12. Golinska P, Ahmed L, Wang D, Goodfellow M. Streptacidiphilus durhamensis sp. nov., isolated from a spruce forest soil. Antonie van Leeuwenhoek 2013; 104:199–206 [View Article] [PubMed]
     [Google Scholar]
  13. Golinska P, Kim BY, Dahm H, Goodfellow M. Streptacidiphilus hamsterleyensis sp. nov., isolated from a spruce forest soil. Antonie van Leeuwenhoek 2013; 104:965–972 [View Article] [PubMed]
     [Google Scholar]
  14. Lee SD. Actinocorallia cavernae sp. nov., isolated from a natural cave in Jeju, Korea. Int J Syst Evol Microbiol 2006; 56:1085–1088 [View Article] [PubMed]
     [Google Scholar]
  15. Seo JP, Yun YW, Lee SD. Nocardia speluncae sp. nov., isolated from a cave. Int J Syst Evol Microbiol 2007; 57:2932–2935 [View Article] [PubMed]
     [Google Scholar]
  16. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  17. Küster E, Williams ST. Selection of media for isolation of Streptomycetes. Nature 1964; 202:928–929 [View Article]
     [Google Scholar]
  18. Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ et al. Genetic Manipulation of Streptomyces. A Laboratory Manual Norwich: John Innes Foundation; 1985
     [Google Scholar]
  19. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [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. 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]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  23. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article]
     [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
     [Google Scholar]
  26. Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D14 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Terlouw BR, Blin K, Navarro-Muñoz JC, Avalon NE, Chevrette MG et al. MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Res 2023; 51:D603–D610 [View Article] [PubMed]
     [Google Scholar]
  31. Lee SD, Schumann P. Specibacter cremeus gen. nov., sp. nov., a new member of the family Micrococcaceae isolated from a natural cave. Int J Syst Evol Microbiol 2019; 69:1767–1774 [View Article] [PubMed]
     [Google Scholar]
  32. MacFaddin JF. Biochemical Tests for Identification of Medical Bacteria, 2nd edn Baltimore: Williams & Wilkins; 1980
     [Google Scholar]
  33. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [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. Saddler GS, Tavecchia P, Lociuro S, Zanol M, Colombo L et al. Analysis of madurose and other actinomycete whole cell sugars by gas chromatography. J Microbiol Methods 1991; 14:185–191 [View Article]
     [Google Scholar]
  36. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  37. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
     [Google Scholar]
  38. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 173–199
     [Google Scholar]
  39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  40. 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]
  41. Hopwood DA. Streptomyces in Nature and Medicine. In The Antibiotic Maker Oxford University Press; 2007 [View Article]
     [Google Scholar]
  42. Sun C, Yang Z, Zhang C, Liu Z, He J et al. Genome mining of Streptomyces atratus SCSIO ZH16: discovery of atratumycin and identification of its biosynthetic gene cluster. Org Lett 2019; 21:1453–1457 [View Article] [PubMed]
     [Google Scholar]
  43. Brian P, Riggle PJ, Santos RA, Champness WC. Global negative regulation of Streptomyces coelicolor antibiotic synthesis mediated by an absA-encoded putative signal transduction system. J Bacteriol 1996; 178:3221–3231 [View Article] [PubMed]
     [Google Scholar]
  44. Reusser F. Rubradirin, an inhibitor of ribosomal polypeptide biosynthesis. Biochemistry 1973; 12:1136–1142 [View Article]
     [Google Scholar]
  45. Yarlagadda V, Medina R, Wright GD. Venturicidin a, a membrane-active natural product inhibitor of ATP synthase potentiates aminoglycoside antibiotics. Sci Rep 2020; 10:8134 [View Article] [PubMed]
     [Google Scholar]
  46. Bieber B, Nüske J, Ritzau M, Gräfe U. Alnumycin a new naphthoquinone antibiotic produced by an endophytic Streptomyces sp. J Antibiot 1998; 51:381–382 [View Article]
     [Google Scholar]
  47. Wang W, Feng M, Li X, Chen F, Zhang Z et al. Antibacterial Activity of aureonuclemycin produced by Streptomyces aureus strain SPRI-371. Molecules 2022; 27:5041 [View Article]
     [Google Scholar]
  48. Wang B, Ren J, Li L, Guo F, Pan G et al. Kinamycin biosynthesis employs a conserved pair of oxidases for B-ring contraction. Chem Commun 2015; 51:8845–8848 [View Article]
     [Google Scholar]
  49. Teufel R, Kaysser L, Villaume MT, Diethelm S, Carbullido MK et al. One-pot enzymatic synthesis of merochlorin A and B. Angew Chem Int Ed 2014; 53:11019–11022 [View Article]
     [Google Scholar]
  50. Qin Z, Munnoch JT, Devine R, Holmes NA, Seipke RF et al. Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants. Chem Sci 2017; 8:3218–3227 [View Article] [PubMed]
     [Google Scholar]
  51. Wolf H, Chinali G, Parmeggiani A. Kirromycin, an inhibitor of protein biosynthesis that acts on elongation factor Tu. Proc Natl Acad Sci USA 1974; 71:4910–4914 [View Article] [PubMed]
     [Google Scholar]
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Streptacidiphilus alkalitolerans sp. nov., Streptacidiphilus cavernicola sp. nov. and Streptacidiphilus jeojiensis sp. nov. isolated from a cave, and an emended description of the genus Streptacidiphilus
Int J Syst Evol Microbiol 75, 006652 (2025); https://doi.org/10.1099/ijsem.0.006652
/content/journal/ijsem/10.1099/ijsem.0.006652
/content/journal/ijsem/10.1099/ijsem.0.006652
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