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Nocardioides speluncae sp. nov., a novel actinobacterium isolated from a karstic subterranean environment sample

  • Bao-Zhu Fang
  • Ming-Xian Han
  • Jian-Yu Jiao
  • Xiao-Tong Zhang
  • Yuan-Guo Xie
  • Wael N. Hozzein
  • Dalal Hussien M. Alkhalifah
  • Min XiaoEmail author
  • Wen-Jun LiEmail author
Original Paper

Abstract

A novel actinobacterial strain, designated YIM ART13T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, South western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were found to aerobic and Gram-stain positive. On the basis of 16S rRNA gene sequence analysis, strain YIM ART13T was found to be closely related to Nocardioides pakistanensis NCCP 1340T (96.1% sequence similarity) and is therefore considered to represent a member of the genus Nocardioides. In addition, ll-diaminopimelic acid was identified as the diagnostic diamino acid in the cell wall peptidoglycan. The whole cell sugars were found to be mannose, galactose, glucose and ribose. The major isoprenoid quinone was identified as MK-8(H4), while the major fatty acids (> 10%) were identified as iso-C16:0, C18:1ω9c and C18:0 10-methyl. The polar lipids were found to contain diphosphatidylglycerol, phosphatidylglycerol phosphatidylinositol and phosphatidylinositol mannoside, an unidentified phospholipid. The genomic DNA G+C content of strain YIM ART13T was determined from the draft genome sequence to be 70.1 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain YIM ART13T represents a novel species of the genus Nocardioides, for which the name Nocardioides speluncae sp. nov. is proposed. The type strain is YIM ART13T (= KCTC 39593T = DSM 100493T).

Keywords

Nocardioides speluncae sp. nov. Karst cave Polyphasic taxonomy 

Notes

Acknowledgements

This research was supported by National Key R&D Program of China (No. 2017YFD0200503), Natural Science Foundation of China (No. 31600015), Natural Science Foundation of Guangdong Province, China (No. 2016A030312003). This work was funded by the Deanship of Scientific Research at Princess Nourah bint Abdulrahman University, through the Research Groups Program Grant no. (RGP-1438-0004).

Author’s contributions

WJL, WH and BZF designed research and project outline. MXH, MX and YGX performed isolation, deposition and identification. JYJ and XTZ performed genome analysis. BZF, DHA and WJL drafted the manuscript. All authors read and approved the final manuscript.

Conflict of interest

The authors declare that they have no direct or indirect conflict of interest.

Supplementary material

10482_2018_1217_MOESM1_ESM.docx (1.2 mb)
Supplementary material 1 (DOCX 1267 kb)

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life SciencesSun Yat-Sen UniversityGuangzhouPeople’s Republic of China
  2. 2.State Key Laboratory of Biogeology and Environmental GeologyChina University of GeosciencesWuhanPeople’s Republic of China
  3. 3.Bioproducts Research Chair, Zoology Department, College of ScienceKing Saud UniversityRiyadhKingdom of Saudi Arabia
  4. 4.Botany and Microbiology Department, Faculty of ScienceBeni-Suef UniversityBeni-SuefEgypt
  5. 5.Biology Department, Faculty of SciencePrincess Nourah bint Abdulrahman UniversityRiyadhKingdom of Saudi Arabia
  6. 6.College of FisheriesHenan Normal UniversityXinxiangPeople’s Republic of China

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