Skip to main content
Log in

Nocardia panacis sp. nov., a novel actinomycete with antiphytopathogen activity isolated from the rhizosphere of Panax notoginseng

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

Strain YIM PH21724T was isolated from the rhizosphere of Panax notoginseng. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain exhibits close phylogenetic relatedness to Nocardia kroppenstedtii N1286T (97.70%), Nocardia farcinica NCTC 11134T (97.67%) and Nocardia puris DSM 44599T (97.40%). The menaquinones were identified as MK-9 (H4), MK-8 (H4, ω-cyclo) and MK-8 (H4), and the major fatty acids (> 10%) were identified as C16:0, C18:1 ω9c and C18:0 10-methyl. The polar lipids were found to be composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified lipid. The G + C content of the genomic DNA was determined to be 67.01 mol%. The phenotypic, chemotaxonomic, phylogenetic and genomic results clearly show strain YIM PH21724T should be classified in the genus Nocardia and represents a novel species, for which the name Nocardia panacis sp. nov. is proposed. The type strain is YIM PH21724T (= DSM 105904T = KCTC 49030T = CCTCC AA 2017043T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Abbreviations

ISP:

International Streptomyces Project

MK:

Menaquinone

References

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu X, Meyer AD, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 48:459–470

    Article  CAS  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    Article  CAS  PubMed  Google Scholar 

  • Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP, Xu LH, Jiang CL (2001) Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51:357–363

    Article  CAS  PubMed  Google Scholar 

  • Ding P, Bai JL, Wang TT, Sun Y, Cao CL, Jiang JH, Qin S (2018) Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil. Int J Syst Evol Microbiol 68:192–197

    Article  CAS  PubMed  Google Scholar 

  • Emms D, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16:157

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ezeoke I, Klenk HP, Pötter G, Schumann P, Moser BD, Lasker BA, Nicholson A, Brown JM (2013) Nocardia amikacinitolerans sp. nov., an amikacin-resistant human pathogen. Int J Syst Evol Microbiol 63:1056–1061

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416

    Article  Google Scholar 

  • Goodfellow M, Maldonado LA (2012) Genus I. Nocardia Trevisan 1889AL. In: Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology (the actinobacteria), Part A, vol 5, 2nd edn. Springer, New York, pp 399–442

    Chapter  Google Scholar 

  • Gordon RE, Barnett DA, Handerhan JE, Pang CHN (1974) Nocardia coeliaca, Nocardia autotrophica and the nocardin strain. Int J Syst Bacteriol 24:54–63

    Article  Google Scholar 

  • Hara S, Ishikawa N, Hara Y, Nehira T, Sakai K, Gonoi T, Ishibashi M (2017) Nabscessins A and B, aminocyclitol derivatives from Nocardia abscessus IFM 10029T. J Nat Prod 80:565–568

    Article  CAS  PubMed  Google Scholar 

  • Jones AL, Fisher AJ, Mahida R, Gould K, Perry JD, Hannan MM, Judge EP, Brown R, Boagey K, Goodfellow M (2014) Nocardia kroppenstedtii sp. nov., an actinomycete isolated from a lung transplant patient with a pulmonary infection. Int J Syst Evol Microbiol 64:751–754

    Article  PubMed  Google Scholar 

  • Kageyama A, Yazawa K, Mukai A, Kinoshita M, Takata N, Nishimura K, Kropperstedt RM, Mikami Y (2004) Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan. Int J Syst Evol Microbiol 54:1927–1931

    Article  CAS  PubMed  Google Scholar 

  • Kavitha A, Prabhakar P, Narasimhulu M, Vijayalakshmi M, Venkateswarlu Y, Rao KV, Raju VBS (2010) Isolation, characterization and biological evaluation of bioactive metabolites from Nocardia levis MK-VL_113. Microbiol Res 165:199–210

    Article  CAS  PubMed  Google Scholar 

  • Kelly KL (1964) Inter-society color council-national bureau of standards color-name charts illustrated with centroid colors published in US. US Government Printing Office, Washington, DC

    Google Scholar 

  • Komaki H, Tanaka KY, Takagi H, Ando A, Nagata Y, Mikami Y (2000) Antitumor activity of brasilicardin A, a novel terpenoid antibiotic from Nocardia brasiliensis. J Antibiot 53:75–77

    Article  CAS  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367

    Article  CAS  Google Scholar 

  • Kroppenstedt RM, Goodfellow M (2006) The Family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillospora and Thermomonospora. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria, vol 3, 3rd edn. Springer, New York, pp 682–724

    Chapter  Google Scholar 

  • Kuchibiro T, Ikeda T, Nakanishi H, Morishita Y, Houdai K, Ito J, Gonoi T (2016) First case report of pulmonary nocardiosis caused by Nocardia Mexicana. JMM Case Rep 3(4):e005054

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lechevalier MP, Lechevalier H (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443

    Article  CAS  Google Scholar 

  • Li W, Yang XQ, Yang YB, Qin SH, Li QL, Zhao LX, Ding ZT (2015) A new natural nucleotide and other antibacterial metabolites from an endophytic Nocardia sp. Nat Prod Res 29:132–136

    Article  CAS  PubMed  Google Scholar 

  • Li QQ, Han MX, Fang BZ, Jiao JY, Liu L, YangZW Zhang WQ, WeiDQ Li WJ (2017) Nocardia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. Int J Syst Evol Microbiol 67:2998–3003

    Article  CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  • Miao CP, Qiao XG, Zheng YK, Chen YW, Xu LH, Gan HL, Zhao LX (2015) First report of Fusarium flocciferum causing root rot of Sanqi (Panax notoginseng) in Yunnan, China. Plant Dis 99:1650

    Article  Google Scholar 

  • Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95

    Article  CAS  Google Scholar 

  • Minnkin DE, Hutchinson IG, Caldicott AB, Goodfellow M (1980) Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 188:221–233

    Article  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note 101, MIDI Inc, Newark, DE

  • Sharma P, Kalita MC, Thakur D (2016) Broad spectrum antimicrobial activity of forest-derived soil actinomycete, Nocardia sp PB-52. Front Microbiol 7:347

    PubMed  PubMed Central  Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Smith LM, Galvin SR (2015) Nocardia puris brain abscess in an immunocompromised woman. JMM Case Rep. https://doi.org/10.1099/jmmcr.0.000020

    Article  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Toru H, Masayuki T, Seiichi T (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29(4):319–322

    Article  Google Scholar 

  • Trevisan V (1889) I Generi e le Specie delle Batteriacee. Zanaboni and Gabuzzi, Milan

    Google Scholar 

  • Waksman SA (1967) The actinomycetes a summary of current knowledge. Ronald Press, New York

    Google Scholar 

  • Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813

    CAS  PubMed  Google Scholar 

  • Xu LH, Li WJ, Liu ZH, Jiang CL (2007) Actinomycete systematic-principle, methods and practice. Science Press, Beijing, pp 40–53

    Google Scholar 

  • Yassin AF, Sträubler B, Schumann P, Schaal KP (2003) Nocardia puris sp. nov. Int J Syst Evol Microbiol 53:1595–1599

    Article  CAS  PubMed  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing EzBio-Cloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286

    Article  CAS  PubMed  Google Scholar 

  • Zhi XY, Li WJ, Stackebrandt E (2009) An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59:589–608

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This research was supported by the National Natural Science Foundation of China (Nos. 31570012, 31660004, 41661069, 31660532).

Author information

Authors and Affiliations

Authors

Contributions

Study conception or design: JYH and CPM. Performing of research: JYH, LL and GP. Data analysis: YQL, LHX and HLG. Writing of this paper: JYH, LXZ and CPM. All authors discussed the results and revised the manuscript.

Corresponding authors

Correspondence to Li-Xing Zhao or Cui-Ping Miao.

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interests in the manuscript.

Ethical statement

This study does not describe any experimental work related to human.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 4043 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hu, JY., Li, L., Peng, G. et al. Nocardia panacis sp. nov., a novel actinomycete with antiphytopathogen activity isolated from the rhizosphere of Panax notoginseng. Antonie van Leeuwenhoek 113, 165–174 (2020). https://doi.org/10.1007/s10482-019-01326-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-019-01326-z

Keywords

Navigation