1887

Abstract

A Gram-negative, non-motile, strictly aerobic and rod- or filamentous-shaped strain, CJU-R4, was isolated from a flower of royal azalea () collected in the Republic of Korea. Strain CJU-R4 was catalase-positive and oxidase-negative, and grew at 15–33 °C (optimum, 28–20 °C), at pH 5.0–8.0 (optimum, pH 7.0–8.0), and in the presence of 0–1 % NaCl (w/v; optimum, 0 %). Strain CJU-R4 had the highest 16S rRNA gene sequence similarity to RHs22 (96.6 %), revealing less than 93 % sequence similarity to other type strains. Phylogenetic and phylogenomic analysis also revealed strain CJU-R4 formed a robust cluster with RHs22. The major fatty acids were summed feature 3 (comprising C 7 and/or C 6; 33.0 %), C 5 (22.1 %), iso-C (12.6 %) and C (10.7 %). The polar lipids were composed of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified phospholipid and four unidentified lipids. Menaquinone-7 was detected as the sole respiratory quinone. The genomic DNA G+C content was 55.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain CJU-R4 and DSM 28354 were 81.5 and 23.9 %, respectively. Based on the results of the phenotypic and genotypic analyses, strain CJU-R4 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CJU-R4 (=KACC 21264=NBRC 114513).

Funding
This study was supported by the:
  • National Institute of Agricultural Sciences (Award PJ013549)
    • Principle Award Recipient: Soon-WoKwon
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/content/journal/ijsem/10.1099/ijsem.0.005306
2022-03-29
2022-05-18
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References

  1. Migula W. Über ein neues System der Bakterien. In Klein L, Migula W. eds Arbeiten Aus Dem Bakteriologischen Institut Der Technischen Hochschule Zu Karlsruhe 1894 pp 235–238
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  3. Finster KW, Herbert RA, Lomstein BA. Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 2009; 59:839–844 [View Article] [PubMed]
    [Google Scholar]
  4. Ten LN, Xu J-L, Jin F-X, Im W-T, Oh H-M et al. Spirosoma panaciterrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:331–335 [View Article] [PubMed]
    [Google Scholar]
  5. Ahn J-H, Weon H-Y, Kim S-J, Hong S-B, Seok S-J et al. Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 2014; 64:3230–3234 [View Article] [PubMed]
    [Google Scholar]
  6. Lee J-J, Srinivasan S, Lim S, Joe M, Im S et al. Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil. Curr Microbiol 2014; 69:286–291 [View Article] [PubMed]
    [Google Scholar]
  7. Lee J-J, Kang M-S, Joo ES, Kim MK, Im W-T et al. Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil. J Microbiol 2015; 53:429–434 [View Article] [PubMed]
    [Google Scholar]
  8. Yang SS, Tang K, Zhang X, Wang J, Wang X et al. Spirosoma soli sp. nov., isolated from biological soil crusts. Int J Syst Evol Microbiol 2016; 66:5568–5574 [View Article] [PubMed]
    [Google Scholar]
  9. Joo ES, Kim EB, Jeon SH, Srinivasan S, Kim MK. Spirosoma swuense sp. nov., isolated from wet soil. Int J Syst Evol Microbiol 2017; 67:532–536 [View Article] [PubMed]
    [Google Scholar]
  10. Li W, Lee S-Y, Park S, Kim B-O, Ten LN et al. Spirosoma lituiforme sp. nov., isolated from soil. J Microbiol 2017; 55:856–861
    [Google Scholar]
  11. Okiria J, Ten LN, Park S-J, Lee S-Y, Lee DH et al. Spirosoma migulaei sp. nov., isolated from soil. J Microbiol 2017; 55:927–932 [View Article]
    [Google Scholar]
  12. Zou R, Zhang Y, Zhou X, Wang Y, Peng F. Spirosoma flavum sp. nov., isolated from Arctic tundra soil. Int J Syst Evol Microbiol 2017; 67:4911–4916 [View Article] [PubMed]
    [Google Scholar]
  13. Li W, Ten LN, Lee S-Y, Kang I-K, Jung H-Y. Spirosoma horti sp. nov., isolated from apple orchard soil. Int J Syst Evol Microbiol 2018; 68:930–935 [View Article] [PubMed]
    [Google Scholar]
  14. Li W, Lee S-Y, Kang I-K, Ten LN, Jung H-Y. Spirosoma agri sp. nov., isolated from apple orchard soil. Curr Microbiol 2018; 75:694–700 [View Article]
    [Google Scholar]
  15. Li W, Lee S-Y, Kang I-K, Ten LN, Jung H-Y. Spirosoma pomorum sp. nov., isolated from apple orchard soil. J Microbiol 2018; 56:90–96 [View Article] [PubMed]
    [Google Scholar]
  16. Li W, Ten LN, Lee S-Y, Lee DH, Jung H-Y. Spirosoma jeollabukense sp. nov., isolated from soil. Arch Microbiol 2018; 200:431–438 [View Article]
    [Google Scholar]
  17. Ten LN, Okiria J, Lee J-J, Lee S-Y, Park S et al. Spirosoma terrae sp. nov., isolated from soil from Jeju Island, Korea. Curr Microbiol 2018; 75:492–498 [View Article]
    [Google Scholar]
  18. Weilan L, Lee J-J, Lee S-Y, Park S, Ten LN et al. Spirosoma humi sp. nov., isolated from soil in South Korea. Curr Microbiol 2018; 75:328–335 [View Article]
    [Google Scholar]
  19. Kang H, Cha I, Kim H, Joh K. Spirosoma telluris sp. nov. and Spirosoma arboris sp. nov. isolated from soil and tree bark, respectively. Int J Syst Evol Microbiol 2020; 70:5355–5362 [View Article] [PubMed]
    [Google Scholar]
  20. Park Y, Maeng S, Damdintogtokh T, Zhang J, Kim M-K et al. Spirosoma profusum sp. nov., and Spirosoma validum sp. nov., radiation-resistant bacteria isolated from soil in South Korea. Antonie van Leeuwenhoek 2021; 114:1155–1164 [View Article]
    [Google Scholar]
  21. Elderiny N, Ten LN, Lee J-J, Lee S-Y, Park S et al. Spirosoma daeguensis sp. nov., isolated from beach soil. J Microbiol 2017; 55:678–683 [View Article]
    [Google Scholar]
  22. Lee J-J, Elderiny N, Lee S-Y, Lee DS, Kim MK et al. Spirosoma gilvum sp. nov., isolated from beach soil. Curr Microbiol 2017; 74:1425–1431 [View Article]
    [Google Scholar]
  23. Okiria J, Ten LN, Lee J-J, Lee S-Y, Cho Y-J et al. Spirosoma litoris sp. nov., a bacterium isolated from beach soil. Int J Syst Evol Microbiol 2017; 67:4986–4991 [View Article] [PubMed]
    [Google Scholar]
  24. Ten LN, Okiria J, Lee J-J, Lee S-Y, Kang I-K et al. Spirosoma koreense sp. nov., a species of the family Cytophagaceae isolated from beach soil. Int J Syst Evol Microbiol 2017; 67:5198–5204 [View Article] [PubMed]
    [Google Scholar]
  25. Ten LN, Elderiny N, Lee J-J, Lee S-Y, Park S et al. Spirosoma harenae sp. nov., a bacterium isolated from a sandy beach. Curr Microbiol 2018; 75:179–185 [View Article]
    [Google Scholar]
  26. Baik KS, Kim MS, Park SC, Lee DW, Lee SD et al. Spirosoma rigui sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2007; 57:2870–2873 [View Article]
    [Google Scholar]
  27. Hatayama K, Kuno T. Spirosoma fluviale sp. nov., isolated from river water. Int J Syst Evol Microbiol 2015; 65:3447–3450 [View Article] [PubMed]
    [Google Scholar]
  28. Lee J-J, Lee Y-H, Park S-J, Lee S-Y, Kim B-O et al. Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 2017; 67:1359–1365 [View Article] [PubMed]
    [Google Scholar]
  29. Li Y, Ai M-J, Sun Y, Zhang Y-Q, Zhang J-Q. Spirosoma lacussanchae sp. nov., a phosphate-solubilizing bacterium isolated from a freshwater reservoir. Int J Syst Evol Microbiol 2017; 67:3144–3149 [View Article] [PubMed]
    [Google Scholar]
  30. Lee J-J, Lee YH, Park SJ, Lim S, Jeong S-W et al. Spirosoma fluminis sp. nov., a gamma-radiation resistant bacterium isolated from sediment of the Han river in South Korea. Curr Microbiol 2016; 73:689–695 [View Article] [PubMed]
    [Google Scholar]
  31. Lee J-J, Park S-J, Lee Y-H, Lee S-Y, Park S et al. Spirosoma luteolum sp. nov. isolated from water. J Microbiol 2017; 55:247–252 [View Article]
    [Google Scholar]
  32. Kim S-J, Ahn J-H, Weon H-Y, Hong S-B, Seok S-J et al. Spirosoma aerophilum sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 2016; 66:2342–2346 [View Article] [PubMed]
    [Google Scholar]
  33. Joo ES, Lee J-J, Cha S, Jheong W, Seo T et al. Spirosoma pulveris sp. nov., a bacterium isolated from a dust sample collected at Chungnam province, South Korea. J Microbiol 2015; 53:750–755 [View Article] [PubMed]
    [Google Scholar]
  34. Kim D-U, Lee H, Kim S-G, Ahn J-H, Yoon Park S et al. Spirosoma aerolatum sp. nov., isolated from a motor car air conditioning system. Int J Syst Evol Microbiol 2015; 65:4003–4007 [View Article] [PubMed]
    [Google Scholar]
  35. Kim D-U, Lee H, Lee S, Park S, Yoon J-H et al. Spirosoma carri sp. nov., isolated from an automobile air conditioning system. Int J Syst Evol Microbiol 2017; 67:4195–4199 [View Article] [PubMed]
    [Google Scholar]
  36. Lee H, Kim D-U, Lee S, Park S, Yoon J-H et al. Spirosoma metallicus sp. nov., isolated from an automobile air conditioning system. J Microbiol 2017; 55:673–677 [View Article] [PubMed]
    [Google Scholar]
  37. Kim D-U, Lee H, Lee S, Park S, Yoon J-H et al. Spirosoma metallilatum sp. nov., isolated from an automotive air conditioning system. Int J Syst Evol Microbiol 2018; 68:523–528 [View Article] [PubMed]
    [Google Scholar]
  38. Fries J, Pfeiffer S, Kuffner M, Sessitsch A. Spirosoma endophyticum sp. nov., isolated from Zn- and Cd-accumulating Salix caprea . . Int J Syst Evol Microbiol 2013; 63:4586–4590 [View Article] [PubMed]
    [Google Scholar]
  39. Ambika Manirajan B, Suarez C, Ratering S, Rusch V, Geissler-Plaum R et al. Spirosoma pollinicola sp. nov., isolated from pollen of common hazel (Corylus avellana L.). Int J Syst Evol Microbiol 2018; 68:3248–3254 [View Article] [PubMed]
    [Google Scholar]
  40. Slabova OI, Nikitin DI. Influence of the incubation temperature on the reaction of oligotrophic bacteria to stress. Microbiology 2004; 73:650–653 [View Article]
    [Google Scholar]
  41. Lyautey E, Jackson CR, Cayrou J, Rols JL, Garabétian F. Bacterial community succession in natural river biofilm assemblages. Microb Ecol 2005; 50:589–601 [View Article] [PubMed]
    [Google Scholar]
  42. Lee JJ, Joo ES, Lee DH, Jung HY, Kim MK. Phylogenetic diversity and UV resistance analysis of radiation-resistant bacteria isolated from the water in Han River. Kor J Microbiol 2016; 52:65–73 [View Article]
    [Google Scholar]
  43. Tahon G, Lebbe L. Spirosoma utsteinense sp. nov. isolated from antarctic ice-free soils from the Utsteinen region, East Antarctica. Int J Syst Evol Microbiol 2021; 71:004754
    [Google Scholar]
  44. Felske A, Rheims H, Wolterink A, Stackebrandt E, Akkermans ADL. Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology 1997; 143:2983–2989 [View Article] [PubMed]
    [Google Scholar]
  45. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  46. 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]
  47. 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]
  48. 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]
  49. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  50. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  51. 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]
  52. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 1992; 9:678–687 [View Article] [PubMed]
    [Google Scholar]
  53. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  54. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  55. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  56. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
  57. 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]
  58. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  59. 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:D206–14 [View Article] [PubMed]
    [Google Scholar]
  60. Dueholm MS, Albertsen M, Otzen D, Nielsen PH, Webber MA. Curli functional amyloid systems are phylogenetically widespread and display large diversity in operon and protein structure. PLoS ONE 2012; 7:e51274 [View Article]
    [Google Scholar]
  61. Kharadi RR, Sundin GW. Dissecting the process of xylem colonization through biofilm formation in Erwinia amylovora . J Plant Pathol 2020; 103:41–49 [View Article]
    [Google Scholar]
  62. Smibert R, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, WA W, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  63. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  64. 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]
  65. Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Methods Microbiol 2011; 38:101–129
    [Google Scholar]
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