Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 73, Issue 7

sp. nov., isolated from weathered potash tailings soil No Access

Abstract

A Gram-positive, aerobic actinomycete, designated strain KLBMP 9356, was isolated from weathered potash tailings soil sampled in Xuzhou, Jiangsu Province, PR China. The colonies were cream-coloured, convex and rounded. The optimal growth conditions of strain KLBMP 9356 were 1 % (w/v) NaCl, 28 °C and pH 7. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KLBMP 9356 showed the highest similarity to CGMCC 1.11084 (98.9 %) and CGMCC 1.11097 (98.7 %). Results from two tree-making algorithms supported the position that strain KLBMP 9356 forms a stable clade with CGMCC 1.11084 and CGMCC 1.11097. Strain KLBMP 9356 exhibited low digital DNA-DNA hybridization values with CGMCC 1.11084T (27.6 %) and CGMCC 1.11097 (31.4 %). The average nucleotide identity values between strain KLBMP 9356 and CGMCC 1.11084 and CGMCC 1.11097 were 83.8% and 85.9%, respectively. The peptidoglycan in the cell wall of the novel strain was -2,6-diaminopimelic acid and the predominant menaquinone was MK-8(H). The major fatty acids (>10 %) were Cω8 and Cω9. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, -phospatidylglycerol and phosphatidylinositol. The genomic DNA G+C content was 71.6 mol%. Based on its morphological, chemotaxonomic and phylogenetic characteristics, strain KLBMP 9356 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KLBMP 9356 (=CGMCC 4.7738=NBRC 115493).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Nocardioidaceae , polyphasic analysis , rare actinobacteria and whole genome
Funding
This study was supported by the:
  • Graduate Research and Innovation Projects of Jiangsu Province (Award KYCX21_2608)
    • Principal Award Recipient: LingxiaoLiu
  • Graduate Research and Innovation Projects of Jiangsu Province (Award KYCX21_2609)
    • Principal Award Recipient: YaZhang
  • the State Key Laboratory of Environmental Geochemistry (Award SKLEG2020207)
    • Principal Award Recipient: Cheng-LiangCao
  • Young Scientists Fund (Award 32101519)
    • Principal Award Recipient: LudanLi
  • Key Research Plan of Modern Agriculture of Xuzhou City (Award KC20049)
    • Principal Award Recipient: Cheng-LiangCao
  • Graduate Research and Innovation Projects of Jiangsu Province (Award KYCX22_2826)
    • Principal Award Recipient: NotApplicable
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005967
2023-07-24
2025-12-05

Metrics

Loading full text...

Full text loading...

References

  1. Prauser H. Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 1976; 26:58–65 [View Article]
     [Google Scholar]
  2. Yoon JH, Lee ST, Park YH. Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 1998; 48 Pt 1:187–194 [View Article] [PubMed]
     [Google Scholar]
  3. Wang L, Xue H-P, Zhang D-F, Huang J-K, Liu C et al. Description of Nocardioides jiangsuensis sp. nov., and proposal for reclassification of the genus Marmoricola as Nocardioides. Curr Microbiol 2023; 80:60 [View Article] [PubMed]
     [Google Scholar]
  4. Liu Y-H, Fang B-Z, Mohamad OAA, Zhang Y-G, Jiao J-Y 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]
  5. Chen X-H, Li F, Li F-N, Chen M-S, Yan X-R et al. Nocardioides acrostichi sp. nov., a novel endophytic actinobacterium isolated from leaf of Acrostichum aureum. Antonie van Leeuwenhoek 2021; 114:479–486 [View Article] [PubMed]
     [Google Scholar]
  6. Cho Y, Jang GI, Cho BC. Nocardioides marinquilinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2013; 63:2594–2599 [View Article] [PubMed]
     [Google Scholar]
  7. Wang L, Li J, Zhang G. Nocardioides rotundus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016; 66:1932–1936 [View Article]
     [Google Scholar]
  8. Roh SG, Lee C, Kim M-K, Kang H-J, Kim YS et al. Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2020; 70:2682–2689 [View Article] [PubMed]
     [Google Scholar]
  9. Zhao Y, Liu Q, Kang M-S, Jin F, Yu H et al. Nocardioides ungokensis sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2015; 65:4857–4862 [View Article]
     [Google Scholar]
  10. Wang S, Zhou Y, Zhang G. Nocardioides flavus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:5275–5280 [View Article]
     [Google Scholar]
  11. Zhang D-C, Schumann P, Redzic M, Zhou Y-G, Liu H-C et al. Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:445–450 [View Article] [PubMed]
     [Google Scholar]
  12. Liu Q, Xin Y-H, Liu H-C, Zhou Y-G, Wen Y. Nocardioides szechwanensis sp. nov. and Nocardioides psychrotolerans sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2013; 63:129–133 [View Article] [PubMed]
     [Google Scholar]
  13. Xie F, Yang Y, Ma H, Quan S, Yue D et al. Nocardioides phosphati sp. nov., an actinomycete isolated from a phosphate mine. Int J Syst Evol Microbiol 2017; 67:1522–1528 [View Article] [PubMed]
     [Google Scholar]
  14. Ikunaga Y, Sato I, Grond S, Numaziri N, Yoshida S et al. Nocardioides sp. strain WSN05-2, isolated from a wheat field, degrades deoxynivalenol, producing the novel intermediate 3-epi-deoxynivalenol. Appl Microbiol Biotechnol 2011; 89:419–427 [View Article] [PubMed]
     [Google Scholar]
  15. Jung CM, Broberg C, Giuliani J, Kirk LL, Hanne LF. Characterization of JP-7 jet fuel degradation by the bacterium Nocardioides luteus strain BAFB. J Basic Microbiol 2002; 42:127–131 [View Article] [PubMed]
     [Google Scholar]
  16. Hamamura N, Arp DJ. Isolation and characterization of alkane-utilizing Nocardioides sp. strain CF8. FEMS Microbiol Lett 2000; 186:21–26 [View Article] [PubMed]
     [Google Scholar]
  17. Satsuma K. Mineralization of s-triazine herbicides by a newly isolated Nocardioides species strain DN36. Appl Microbiol Biotechnol 2010; 86:1585–1592 [View Article] [PubMed]
     [Google Scholar]
  18. Piutti S, Semon E, Landry D, Hartmann A, Dousset S et al. Isolation and characterisation of Nocardioides sp. SP12, an atrazine-degrading bacterial strain possessing the gene trzN from bulk- and maize rhizosphere soil. FEMS Microbiol Lett 2003; 221:111–117 [View Article] [PubMed]
     [Google Scholar]
  19. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  20. 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]
     [Google Scholar]
  21. 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]
  22. 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]
     [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. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  25. 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]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  27. Lim HJ, Lee EH, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379–387 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [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. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article] [PubMed]
     [Google Scholar]
  32. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  33. Ley JD, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article]
     [Google Scholar]
  34. Wayne LG. International committee on systematic bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988; 268:433–434 [View Article] [PubMed]
     [Google Scholar]
  35. Ursing JB, Lior H, Owen RJ. Proposal of minimal standards for describing new species of the family Campylobacteraceae. Int J Syst Bacteriol 1994; 44:842–845 [View Article] [PubMed]
     [Google Scholar]
  36. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z 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]
  37. Kurup PV, Schmitt JA. Numerical taxonomy of Nocardia. Can J Microbiol 1973; 19:1035–1048 [View Article] [PubMed]
     [Google Scholar]
  38. Bochner BR. Global phenotypic characterization of bacteria. FEMS Microbiol Rev 2009; 33:191–205 [View Article] [PubMed]
     [Google Scholar]
  39. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  40. Smibert R. Methods for General and Molecular Bacteriology ASM; 1994 pp 607–654
     [Google Scholar]
  41. Edberg SC, Pittman S, Singer JM. The use of bile — esculin agar for the taxonomic classification of the family Enterobacteriaceae. Antonie van Leeuwenhoek 1977; 43:31–35 [View Article]
     [Google Scholar]
  42. Welsh CT. Microbiology: A Laboratory Manual Pearson; 2019
     [Google Scholar]
  43. Qin S, Bai J-L, Wang Y, Feng W-W, Yuan B et al. Tamaricihabitans halophyticus gen. nov., sp. nov., an endophytic actinomycete of the family Pseudonocardiaceae. Int J Syst Evol Microbiol 2015; 65:4662–4668 [View Article] [PubMed]
     [Google Scholar]
  44. Kelly KL, Judd DB. ISCC-NBS Color-Name Charts Illustrated with Centroid Colors Washington; 1965
     [Google Scholar]
  45. Cao C, Sun Y, Wu B, Zhao S, Yuan B et al. Actinophytocola glycyrrhizae sp. nov. isolated from the rhizosphere of Glycyrrhiza inflata. Int J Syst Evol Microbiol 2018; 68:2504–2508 [View Article]
     [Google Scholar]
  46. 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]
  47. 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]
  48. 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]
  49. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. J Chromatogr 1975; 112:594–604
     [Google Scholar]
  50. 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; 69:2329–2334 [View Article] [PubMed]
     [Google Scholar]
  51. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Nocardioides glacieisoli sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2015; 65:4845–4849 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005967
Loading
Nocardioides potassii sp. nov., isolated from weathered potash tailings soil
Int J Syst Evol Microbiol 73, 005967 (2023); https://doi.org/10.1099/ijsem.0.005967
/content/journal/ijsem/10.1099/ijsem.0.005967
/content/journal/ijsem/10.1099/ijsem.0.005967
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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