1887

Abstract

A Gram-stain-positive, aerobic, non-motile, non-spore-forming, coccus-shaped actinobacterium, designated strain 12Sc4-1, was isolated from a soil sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, China. Strain 12Sc4-1 grew at 8‒35 °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 sequence suggested that strain 12Sc4-1 belonged to the genus Nakamurella and shared the highest 16S rRNA gene sequence similarity to Nakamurella silvestris S20-107 (96.94 %). Strain 12Sc4-1 showed <96.0 % 16S rRNA gene sequence similarities to all other recognized members of the genus Nakamurella . Chemotaxonomic analyses showed that the isolate possessed meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan, glucose, mannose and galactose as whole-cell sugars, and MK-8(H4) as the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, phosphatidylinositol, an unidentified phospholipid, an unidentified phosphoglycolipid and an unidentified glycolipid. The major fatty acids were C16 : 0 and anteiso-C15 : 0. The DNA G+C content was 72.1 mol% (draft genome sequence). On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, strain 12Sc4-1 represents a novel species of the genus Nakamurella , for which the name Nakamurella deserti sp. nov. is proposed. The type strain is 12Sc4-1 (=KCTC 49114=CGMCC 1.16555).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003132
2018-11-22
2020-01-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/1/214.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003132&mimeType=html&fmt=ahah

References

  1. Yoshimi Y, Hiraishi A, Nakamura K. Isolation and characterization of Microsphaera multipartita gen. nov., sp. nov., a polysaccharide-accumulating gram-positive bacterium from activated sludge. Int J Syst Bacteriol 1996;46:519–525 [CrossRef]
    [Google Scholar]
  2. Tao TS, Yue YY, Chen WX, Chen WF. Proposal of Nakamurella gen. nov. as a substitute for the bacterial genus Microsphaera Yoshimi et al. 1996 and Nakamurellaceae fam. nov. as a substitute for the illegitimate bacterial family Microsphaeraceae Rainey et al. 1997. Int J Syst Evol Microbiol 2004;54:999–1000 [CrossRef][PubMed]
    [Google Scholar]
  3. Yoon JH, Kang SJ, Jung SY, Oh TK. Humicoccus flavidus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2007;57:56–59 [CrossRef][PubMed]
    [Google Scholar]
  4. Kim KK, Lee KC, Lee JS. Nakamurella panacisegetis sp. nov. and proposal for reclassification of Humicoccus flavidus Yoon et al., 2007 and Saxeibacter lacteus Lee et al., 2008 as Nakamurella flavida comb. nov. and Nakamurella lactea comb. nov. Syst Appl Microbiol 2012;35:291–296 [CrossRef][PubMed]
    [Google Scholar]
  5. Lee SD, Park SK, Yun YW, Lee DW. Saxeibacter lacteus gen. nov., sp. nov., an actinobacterium isolated from rock. Int J Syst Evol Microbiol 2008;58:906–909 [CrossRef][PubMed]
    [Google Scholar]
  6. Tuo L, Li FN, Pan Z, Lou I, Guo M et al. Nakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from the bark of Kandelia candel. Int J Syst Evol Microbiol 2016;66:1577–1582 [CrossRef][PubMed]
    [Google Scholar]
  7. França L, Albuquerque L, Zhang DC, Nouioui I, Klenk HP et al. Nakamurella silvestris sp. nov., an actinobacterium isolated from alpine forest soil. Int J Syst Evol Microbiol 2016;66:5460–5464 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 [CrossRef][PubMed]
    [Google Scholar]
  9. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  10. 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 [CrossRef][PubMed]
    [Google Scholar]
  11. 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 [CrossRef][PubMed]
    [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [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 1874;2016:1870
    [Google Scholar]
  16. 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 [CrossRef][PubMed]
    [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  18. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961;3:208–IN1 [CrossRef]
    [Google Scholar]
  19. 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 [CrossRef][PubMed]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A. Icarus: visualizer for de novo assembly evaluation. Bioinformatics 2016;32:3321–3323 [CrossRef][PubMed]
    [Google Scholar]
  22. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  23. 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 [CrossRef]
    [Google Scholar]
  24. 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]
  25. 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 [CrossRef][PubMed]
    [Google Scholar]
  26. 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 [CrossRef][PubMed]
    [Google Scholar]
  27. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th ed. San Francisco: Benjamin Cummings Pearson Education; 2002
    [Google Scholar]
  28. 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 [CrossRef][PubMed]
    [Google Scholar]
  29. 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]
  30. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  31. 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 [CrossRef][PubMed]
    [Google Scholar]
  32. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972;36:407–477[PubMed]
    [Google Scholar]
  33. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003132
Loading
/content/journal/ijsem/10.1099/ijsem.0.003132
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited articles

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error