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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 1

sp. nov., isolated from Taklamakan desert soil Free

Abstract

A Gram-stain-positive, aerobic, non-motile, rod-shaped actinobacterium, designated strain 21Sc5-5, was isolated from a soil sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China and investigated by using a polyphasic approach. Strain 21Sc5-5 grew at 10–37 °C (optimum, 28–30 °C), pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 0–3 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain 21Sc5-5 formed a distinct lineage within the genus and had the highest similarity to THG-S11.7 (97.30 %), followed by A2-4 (97.22 %), NSP 41 (97.15 %) and MN8 (97.15 %). The results of chemotaxonomic analyses showed that the isolate possessed -diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan and MK-8(H) as the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and three unidentified lipids. The major fatty acids were iso-C and 10-methyl C. The genome length of strain 21Sc5-5 was 4.67 Mb containing 372 contigs and with a DNA G+C content of 70.4 mol%. On the basis of data from phylogenetic, phenotypic and chemotaxonomic analyses, strain 21Sc5-5 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 21Sc5-5 (=JCM 33365=CGMCC 4.7608).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): actinobacteria , Nocardioides vastitatis , strain 21Sc5-5T and taxonomy
Funding
This study was supported by the:
  • CAMS innovation Fund for Medical Sciences (Award 2017- I2M-BandR-08)
  • CAMS innovation Fund for Medical Sciences (Award 2017-I2M-1-012)
© 2020 The Authors
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2019-09-18
2024-04-16
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References

  1. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
     [Google Scholar]
  2. Prauser H. Nocardioides, a new genus of the order actinomycetales. Int J Syst Bacteriol 1976; 26:58–65 [View Article]
     [Google Scholar]
  3. Wang X, Yang J, Lu S, Lai XH, Jin D et al. Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2018; 68:3874–3880 [View Article][PubMed]
     [Google Scholar]
  4. Yan ZF, Lin P, Li CT, Kook M, Yi TH. Nocardioides pelophilus sp. nov., isolated from freshwater mud. Int J Syst Evol Microbiol 2018; 68:1942–1948 [View Article][PubMed]
     [Google Scholar]
  5. Zhang LY, Ming H, Zhao ZL, Ji WL, Salam N et al. Nocardioides allogilvus sp. nov., a novel actinobacterium isolated from a karst cave. Int J Syst Evol Microbiol 2018; 68:2485–2490 [View Article][PubMed]
     [Google Scholar]
  6. Park YJ, Jeong SE, Jung HS, Park SY, Jeon CO. Nocardioides currus sp. nov., isolated from a mobile car air-conditioning system. Int J Syst Evol Microbiol 2018; 68:2977–2982 [View Article][PubMed]
     [Google Scholar]
  7. Wu S, Xia X, Zhou Z, Wang D, Wang G. Nocardioides gansuensis sp. nov., isolated from geopark soil. Int J Syst Evol Microbiol 2019; 69:390–396 [View Article][PubMed]
     [Google Scholar]
  8. Li C, Shi K, Zhang Y, Wang G. Nocardioides silvaticus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:68–73 [View Article][PubMed]
     [Google Scholar]
  9. Liu YH, Fang BZ, Mohamad OAA, Zhang YG, Jiao JY et al. Nocardioides ferulae sp. nov., isolated from root of an endangered medicinal plant Ferula songorica Pall. ex Spreng. Int J Syst Evol Microbiol 2019; 69:1253–1258 [View Article][PubMed]
     [Google Scholar]
  10. Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YH. Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China. Int J Syst Evol Microbiol 2019
     [Google Scholar]
  11. Prauser H. Nocardioides luteus spec. nov. Zeitschrift für allgemeine Mikrobiologie 1984; 24:647–648 [View Article]
     [Google Scholar]
  12. O'Donnell AG, Goodfellow M, Minnikin DE. Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) lochhead in the genus Nocardioides (Prauser) emend. O'Donnell et al. as Nocardioides simplex comb. nov. Arch Microbiol 1982; 133:323–329 [View Article][PubMed]
     [Google Scholar]
  13. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  14. 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]
  15. Magee CM, Rodeheaver G, Edgerton MT, Edlich RF. A more reliable gram staining technic for diagnosis of surgical infections. Am J Surg 1975; 130:341–346 [View Article][PubMed]
     [Google Scholar]
  16. Xu P, Li WJ, 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 [View Article][PubMed]
     [Google Scholar]
  17. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 6th ed. San Francisco: Benjamin Cummings Pearson Education; 2002
     [Google Scholar]
  18. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article][PubMed]
     [Google Scholar]
  19. Kim SJ, Cho H, Joa JH, Hamada M, Ahn JH et al. Nakamurella intestinalis sp. nov., isolated from the faeces of Pseudorhynchus japonicus . Int J Syst Evol Microbiol 2017; 67:2970–2974 [View Article][PubMed]
     [Google Scholar]
  20. Li WJ, Xu P, Schumann P, Zhang YQ, 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]
  21. 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]
  22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 1874; 2016:1870
     [Google Scholar]
  23. 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]
  24. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  26. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  28. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [View Article]
     [Google Scholar]
  29. Chen Y, Chen Y, Shi C, Huang Z, Zhang Y et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 2018; 7:1–6 [View Article][PubMed]
     [Google Scholar]
  30. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  32. 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]
  33. 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]
  34. 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]
  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. Guo L, Tuo L, Habden X, Zhang Y, Liu J et al. Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 2015; 65:206–213 [View Article][PubMed]
     [Google Scholar]
  37. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477[PubMed]
     [Google Scholar]
  38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI inc; 1990
     [Google Scholar]
  39. Singh H, du J, Trinh H, Won K, Yang JE et al. Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. Int J Syst Evol Microbiol 2016; 66:371–378 [View Article][PubMed]
     [Google Scholar]
  40. Yoon JH, Lee JK, Jung SY, Kim JA, Kim HK et al. Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium. Int J Syst Evol Microbiol 2006; 56:1783–1787 [View Article][PubMed]
     [Google Scholar]
  41. Yoon JH, Cho YG, Lee ST, Suzuki K, Nakase T et al. Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. Int J Syst Bacteriol 1999; 49 Pt 2:675–680 [View Article][PubMed]
     [Google Scholar]
  42. Yoon JH, Kang SJ, Park S, Kim W, Oh TK. Nocardioides caeni sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 2009; 59:2794–2797 [View Article][PubMed]
     [Google Scholar]
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Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil
Int J Syst Evol Microbiol 70, 77 (2020); https://doi.org/10.1099/ijsem.0.003718
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