1887

Abstract

A Gram-reaction-positive, strictly aerobic, catalase-positive, oxidase-negative, non-motile actinobacterium, designated C1-24, was isolated from a soil sample collected inside a natural cave. The organism exhibited a rod–coccus developmental cycle during its growth phase. Results of 16S rRNA gene-based phylogenetic analysis showed that the novel strain belonged to the genus and formed a distinct sublineage at the base of the radiation including a cluster. In the results of phylogenomic analysis, the novel strain was loosely associated to . The closest relatives were (98.01 % 16S rRNA gene sequence similarity) and (98.01 %). The genome size was 5.66 Mbp and the DNA G+C content was 64.30 mol%. Whole-cell hydrolysates contained -diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H) was the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid and three unidentified phospholipids. Mycolic acids were present. The major fatty acids were C, C ω9, C ω7 and/or C ω6 and 10-methyl C. Digital DNA–DNA hybridization and average nucleotide identity values revealed that the novel strain should be assigned to a different species. Based on the combined data obtained here, strain C1-24 (=KACC 19964=DSM 109484) represents a new species of the genus , for which sp. nov. is proposed. Also, it is proposed that is a later heterosynonym of based on analyses of 16S rRNA gene and whole-genome sequences.

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2020-06-15
2020-08-06
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References

  1. Zopf W. Uber Ausscheidung von Fettfarbstoffen (Lipochromen) seitens gewisser Spaltpilze. Ber Duet Bot Ges 1891; 9:22–28
    [Google Scholar]
  2. Jones AL, Goodfellow M. Genus Rhodococcus . In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K et al. (editors) Bergey's Manual of Systematic Bacteriology 5, 2nd ed. New York: Springer; 2012 pp 437–464
    [Google Scholar]
  3. Ko KS, Kim Y, Seong CN, Lee SD. Rhodococcus antrifimi sp. nov., isolated from dried bat dung of a cave. Int J Syst Evol Microbiol 2015; 65:4043–4048 [CrossRef][PubMed]
    [Google Scholar]
  4. Lee SD, Kim Y-J, Kim IS. Rhodococcus subtropicus sp. nov., a new actinobacterium isolated from a cave. Int J Syst Evol Microbiol 2019; 69:3128–3134 [CrossRef][PubMed]
    [Google Scholar]
  5. 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 [CrossRef][PubMed]
    [Google Scholar]
  6. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [CrossRef]
    [Google Scholar]
  7. 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]
  8. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 24:4876–4882
    [Google Scholar]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  10. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  12. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  13. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed]
    [Google Scholar]
  16. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [CrossRef]
    [Google Scholar]
  17. 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 [CrossRef][PubMed]
    [Google Scholar]
  18. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  19. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [CrossRef][PubMed]
    [Google Scholar]
  20. Uchida K, Aida . Acyl type of bacterial cell wall: its simple identification by colorimetric method. J Gen Appl Microbiol 1977; 23:249–260 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. Minnikin DE, Patal PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [CrossRef]
    [Google Scholar]
  23. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985. pp 173-–199
    [Google Scholar]
  24. 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 [CrossRef]
    [Google Scholar]
  25. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:12196–19131 [CrossRef][PubMed]
    [Google Scholar]
  26. Táncsics A, Benedek T, Farkas M, Máthé I, Márialigeti K et al. Sequence analysis of 16S rRNA, gyrB and catA genes and DNA-DNA hybridization reveal that Rhodococcus jialingiae is a later synonym of Rhodococcus qingshengii . Int J Syst Evol Microbiol 2014; 64:298–301 [CrossRef][PubMed]
    [Google Scholar]
  27. Švec P, Černohlávková J, Busse H-J, Vojtková H, Pantůček R et al. Classification of strain CCM 4446T as Rhodococcus degradans sp. nov. Int J Syst Evol Microbiol 2015; 65:4381–4387 [CrossRef][PubMed]
    [Google Scholar]
  28. Xu J-L, He J, Wang Z-C, Wang K, Li W-J et al. Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium. Int J Syst Evol Microbiol 2007; 57:2754–2757 [CrossRef][PubMed]
    [Google Scholar]
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