1887

Abstract

A novel actinobacterial strain, designated Z022, isolated from a soil sample collected from Dangxiong in Tibet Autonomous Region (PR China), was determined by polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Strain Z022 showed high similarity value to NBRC 13056 (98.87 %) and subsp NBRC 12735 (98.68 %) based on the 16S rRNA gene phylogenetic tree. The genomic DNA G+C content of strain Z022 based on the genome sequence was 72.16 mol%. DNA–DNA relatedness values between strain Z022 and strain NBRC 13056 was 23.7±1.3 % and significantly lower than 70 %. Chemotaxonomic data revealed that strain Z022 possessed MK-9(H) and MK-9(H) as the predominant menaquinone, -diaminopimelic acid as the diagnostic diamino acid, and galactose, glucose, xylose and ribose as whole cell sugars. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) were the predominant polar lipids; anteiso-C, iso-C, and anteiso-C were the major fatty acids. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z022 (=JCM 31053=CGMCC 4.7273) should be classified in the genus as sp. nov.

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2019-09-01
2024-04-19
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References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341[PubMed]
    [Google Scholar]
  2. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  3. Anderson AS, Wellington EM. The taxonomy of Streptomyces and related genera. Int J Syst Evol Microbiol 2001; 51:797–814 [View Article][PubMed]
    [Google Scholar]
  4. Manfio GP. Towards minimal standards for the description of Streptomyces species. Biotekhnologiya 1995; 8:228–237
    [Google Scholar]
  5. Goodfellow M, Fiedler HP. A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie van Leeuwenhoek 2010; 98:119–142 [View Article][PubMed]
    [Google Scholar]
  6. Bérdy J. Thoughts and facts about antibiotics: where we are now and where we are heading. J Antibiot 2012; 65:385–395 [View Article][PubMed]
    [Google Scholar]
  7. Zhang B, Wu X, Zhang W, Chen X, Zhang G et al. Diversity and succession of actinobacteria in the Forelands of the Tianshan Glacier, China. Geomicrobiol J 2016; 33:716–723 [View Article]
    [Google Scholar]
  8. Zhang B, Tang S, Chen X, Zhang L, Zhang G et al. Streptomyces lacrimifluminis sp. nov., a novel actinobacterium that produces antibacterial compounds, isolated from soil. Int J Syst Evol Microbiol 2016; 66:4981–4986 [View Article][PubMed]
    [Google Scholar]
  9. Zhang B, Tang S, Chen X, Zhang G, Zhang W et al. Streptomyces qaidamensis sp. nov., isolated from sand in the Qaidam Basin, China. J Antibiot 2018; 71:880–886 [View Article][PubMed]
    [Google Scholar]
  10. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  11. Waksman SA. The Actinomycetes . A Summary of Current Knowledge New York: Ronald; 1967
    [Google Scholar]
  12. Kelly KL. ISCC-NBC color-name charts illustrated with centroid colors; 1964
  13. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  14. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the Order Actinomycetales. Int J Syst Bacteriol 1993; 43:805–812 [View Article]
    [Google Scholar]
  15. 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]
  16. Lee HJ, Whang KS. Streptomyces graminifolii sp. nov., isolated from bamboo (Sasa borealis) litter. Int J Syst Evol Microbiol 2014; 64:2517–2521 [View Article][PubMed]
    [Google Scholar]
  17. Eguchi T, Takada N, Nakamura S, Tanaka T, Makino T et al. Streptomyces bungoensis sp. nov. Int J Syst Bacteriol 1993; 43:794–798 [View Article]
    [Google Scholar]
  18. Lin YB, Wang XY, Wang TT, An SS, Shi P et al. Streptomyces ziwulingensis sp. nov., isolated from grassland soil. Int J Syst Evol Microbiol 2013; 63:1545–1549 [View Article][PubMed]
    [Google Scholar]
  19. Lechevalier M. The chemotaxonomy of actinomycetes. Actinomycete taxonomy 1980227–291
    [Google Scholar]
  20. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  21. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  22. Kroppenstedt RM. Separation of bacterial menaquinones by hplc using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [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 [View Article]
    [Google Scholar]
  24. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  25. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  26. Mingma R, Duangmal K, Thamchaipenet A, Trakulnaleamsai S, Matsumoto A et al. Streptomyces oryzae sp. nov., an endophytic actinomycete isolated from stems of rice plant. J Antibiot 2015; 68:368–372 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  29. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  30. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  31. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian Protein Metabolism 1969; 3:21–132
    [Google Scholar]
  32. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  33. Yoon SH, Ha SM, 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]
  34. Chin CS, 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 [View Article][PubMed]
    [Google Scholar]
  35. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article][PubMed]
    [Google Scholar]
  36. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article][PubMed]
    [Google Scholar]
  37. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
  38. Yoon SH, Ha SM, Lim J, Kwon S, 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]
  39. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
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