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Abstract

A polyphasic study was carried out to establish the taxonomic position of an acidophilic isolate designated MMS16-CNU292 (=JCM 32302) from pine grove soil, and provisionally assigned to the genus . On the basis of 16S rRNA gene sequence similarity, the strain formed a novel evolutionary lineage within and showed highest similarities to KCTC 9699 (98.75 %), IFO 15206 (98.74 %), NRRL B-1817 (98.61 %) and HKI 0315 (98.42 %), respectively. Strain MMS16-CNU292 possessed MK-9(H) and MK-9(H) as the major menaquinones, and a major amount of -diaminopimelic acid in the cell-wall peptidoglycan. The whole-cell hydrolysates were rich in galactose, glucose and mannose, and the polar lipids mainly consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides. The major fatty acids were anteiso-C-A, anteiso-C, and iso-C, and the DNA G+C content was 71.5 mol%. The strain exhibited antibacterial activity against a number of bacterial strains, and the activity was generally greater when grown in acidic conditions. The phylogenetic, chemotaxonomic and phenotypic properties enabled distinction of MMS16-CNU292 from related species, and thus the isolate should be recognized as a new species of the genus , for which the name sp. nov. (type strain=MMS16-CNU292=KCTC 49011=JCM 32302) is proposed.

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2020-09-14
2020-11-30
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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 [CrossRef][PubMed]
    [Google Scholar]
  2. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341 [CrossRef][PubMed]
    [Google Scholar]
  3. Kim SB, Lonsdale J, Seong C-N, 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 2003; 83:107–116 [CrossRef][PubMed]
    [Google Scholar]
  4. Takahashi Y, Seino A, Iwai Y, Ōmura S. Taxonomic study and morphological differentiation of an actinomycete genus, Kitasatospora . Zentralbl Bakteriol 1999; 289:265–284 [CrossRef][PubMed]
    [Google Scholar]
  5. Kämpfer P. Genus Incertae sedis I. Kitasatospora . Bergey’s Manual of Systematic Bacteriology 2012; 5:1768–1777
    [Google Scholar]
  6. Takahashi Y. Genus Kitasatospora, taxonomic features and diversity of secondary metabolites. J Antibiot 2017; 70:506–513 [CrossRef][PubMed]
    [Google Scholar]
  7. Uilenberg G, Goff WL. Polyphasic taxonomy. Ann N Y Acad Sci 2006; 1081:492–497 [CrossRef][PubMed]
    [Google Scholar]
  8. Uilenberg G, Thiaucourt F, Jongejan F. On molecular taxonomy: what is in a name?. Exp Appl Acarol 2004; 32:301–312 [CrossRef][PubMed]
    [Google Scholar]
  9. Tsukamura M, Mizuno S, Murata H. Numerical taxonomy study of the taxonomic position of Nocardia rubra reclassified as Gordona lentifragmenta Tsukamura nom. nov. Int J Syst Evol Microbiol 1975; 25:377–382
    [Google Scholar]
  10. Kim M-K, Kim T-W, Kim T-S, Joung Y, Han J-H et al. Fluviicoccus keumensis gen. nov., sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 2016; 66:201–205 [CrossRef][PubMed]
    [Google Scholar]
  11. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA-and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [CrossRef][PubMed]
    [Google Scholar]
  12. 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]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  14. Baba ML, Darga LL, Goodman M, Czelusniak J. Evolution of cytochromec investigated by the maximum parsimony method. J Mol Evol 1981; 17:197–213 [CrossRef][PubMed]
    [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  17. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [CrossRef][PubMed]
    [Google Scholar]
  18. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  19. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [CrossRef]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. 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; 14:60–2105 [CrossRef][PubMed]
    [Google Scholar]
  22. Collins M. Isoprenoid quinone analysis in bacterial classification and identification. Chemical Methods in Bacterial Systematics 1985267–285
    [Google Scholar]
  23. 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]
  24. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
  25. Park J, Kim YR, Kim M-K, Jo JH, Im W-T et al. Humibacter soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:2509–2514 [CrossRef][PubMed]
    [Google Scholar]
  26. Hockett KL, Baltrus DA. Use of the soft-agar overlay technique to screen for bacterially produced inhibitory compounds. J Vis Exp 2017; 119:55064 [CrossRef][PubMed]
    [Google Scholar]
  27. Groth I, Rodríguez C, Schütze B, Schmitz P, Leistner E et al. Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 2004; 54:2121–2129 [CrossRef][PubMed]
    [Google Scholar]
  28. Nakagaito Y, Yokota A, Hasegawa T. Three new species of the genus Streptomyces: Streptomyces cochleatus sp. nov., Streptomyces paracochleatus sp. nov., and Streptomyces azaticus sp. nov. J Gen Appl Microbiol 1992; 38:105–120 [CrossRef]
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
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