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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 8

sp. nov., a Pb-tolerant actinomycete No Access

Abstract

A novel actinobacterium, designated KC 17012, was isolated from lead zinc tailings collected from Lanping, Yunnan, PR China. Comparative 16S rRNA gene sequencing showed that KC 17012 belonged to the genus and was most closely related to the type strains of (98.34%), (98.34%) and (98.27%). Phylogenetic tree analysis revealed strain KC 17012 formed a distinct clade. The genome size was 8.64 Mbp with a DNA G+C content of 70.8%. Digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain KC 17012 and those of JCM 4796 (25.3 and 81.5 %) and NBRC 109811 (30.1 and 85.7 %) were below the thresholds of 70 and 96% for prokaryotic conspecific assignation. The strain formed long straight aerial hyphae which generated regular short rod spores with spiny surfaces. Growth occurred at 10–45 °C, pH 6–8 and with 0–9 % NaCl (w/v). Strain KC 17012 contained -diaminopimelic acid and the major whole-cell hydrolysates included glucose, mannose and ribose. The menaquinones were MK-9(H), MK-9(H) and MK-9(H). The major cellular fatty acids were iso-C, anteiso-C, iso-C and anteiso-C. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified lipid and one unidentified phospholipid. On the basis of the results of a polyphasic taxonomic study, it is concluded that KC 17012 represents a novel species of the genus , for which the name sp. nov., is proposed. The type strain is KC 17012 (CGMCC 4.7704=JCM 35204).

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  • Accepted:
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Keyword(s): Pb2+ -tolerant , phylogenetic analysis and Streptomyces plumbidurans sp. nov.
Funding
This study was supported by the:
  • The Yunnan Ten Thousand Talents Program for Young Top-Notch Talents (Award YNWR-QNBJ-2018-135)
    • Principle Award Recipient: LiangLian-Ming
  • The Yunnan Ten Thousand Talent Plans for Young Top-notch Talents of Yunnan Province (Award YNWR-QNBJ-2018-011)
    • Principle Award Recipient: CaoYan-Ru
  • A grant from State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University (Award 2019KF005)
    • Principle Award Recipient: CaoYan-Ru
  • National Natural Science Foundation of China (Award 31660002)
    • Principle Award Recipient: CaoYan-Ru
  • Joint Special Project of Universities in Yunnan Province (Award 2018FH001-004)
    • Principle Award Recipient: HouXiu-Li
  • Joint Special Project of Universities in Yunnan Province (Award 2018FH001-003)
    • Principle Award Recipient: CaoYan-Ru
© 2022 The Authors
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References

  1. Kämpfer P. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York, USA: Springer; 2012 pp 1679–1680
     [Google Scholar]
  2. Fashola MO, Ngole-Jeme VM, Babalola OO. Heavy metal pollution from gold mines: environmental effects and bacterial strategies for resistance. Int J Environ Res Public Health 2016; 13:1–20 [View Article] [PubMed]
     [Google Scholar]
  3. Gadd GM. Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology 2010; 156:609–643 [View Article] [PubMed]
     [Google Scholar]
  4. El Baz S, Baz M, Barakate M, Hassani L, El Gharmali A et al. Resistance to and accumulation of heavy metals by actinobacteria isolated from abandoned mining areas. Sci World J 2015; 2015:1–14 [View Article] [PubMed]
     [Google Scholar]
  5. Puranik PR, Chabukswar NS, Paknikar KM. Cadmium biosorption by Streptomyces pimprina waste biomass. Appl Microbiol Biotechnol 1995; 43:1118–1121 [View Article]
     [Google Scholar]
  6. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  7. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. 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]
  10. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  13. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article] [PubMed]
     [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
     [Google Scholar]
  17. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. 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]
  20. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  21. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  22. Kelly KL. Inter-Society Color Council – National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  23. Murray RGE, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. Methods for General and Molecular Bacteriology Washington: American Society for Microbiology; 1994 pp 22–41
     [Google Scholar]
  24. Smibert RM, Krieg NR. Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp 409–443
     [Google Scholar]
  25. Xu P, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153
     [Google Scholar]
  26. Smibert RM, Kreig 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 pp 607–654
     [Google Scholar]
  27. Kurup PV, Schmitt JA. Numerical taxonomy of Nocardia. Can J Microbiol 1973; 19:1035–1048 [View Article] [PubMed]
     [Google Scholar]
  28. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  29. 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]
  30. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  31. Tang S-K, Wang Y, Chen Y, Lou K, Cao L-L et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 2009; 59:2025–2031 [View Article] [PubMed]
     [Google Scholar]
  32. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
     [Google Scholar]
  33. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  34. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  35. 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]
  36. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
     [Google Scholar]
  37. Liu C, Wang X, Yan Y, Wang J, Zhang B et al. Streptomyces heilongjiangensis sp. nov., a novel actinomycete that produces borrelidin isolated from the root surface of soybean [Glycine max (L.) Merr]. Int J Syst Evol Microbiol 2013; 63:1030–1036 [View Article] [PubMed]
     [Google Scholar]
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Streptomyces plumbidurans sp. nov., a Pb2+-tolerant actinomycete
Int J Syst Evol Microbiol 72, 005505 (2022); https://doi.org/10.1099/ijsem.0.005505
/content/journal/ijsem/10.1099/ijsem.0.005505
/content/journal/ijsem/10.1099/ijsem.0.005505
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