Skip to main content
SpringerLink
Log in

Nocardia rhizosphaerae sp. nov., a novel actinomycete isolated from the coastal rhizosphere of Artemisia Linn., China

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

Abstract

A novel actinomycete, designated strain KLBMP S0043T, was isolated from the rhizosphere soil of Artemisia Linn. collected from the coastal region of Lianyungang, Jiangsu Province, in east China and was studied in detail for its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain KLBMP S0043T is a member of the genus Nocardia. The 16S rRNA gene sequence similarity indicated that strain KLBMP S0043T is closely related to Nocardia asteroides NBRC 15531T (97.61 %) and Nocardia neocaledoniensis SBHR OA6T (97.38 %); similarity to other type strains of the genus Nocardia was found to be less than 97.2 %. The organism has chemical and morphological features consistent with its classification in the genus Nocardia such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall peptidoglycan and arabinose and galactose as the diagnostic sugars. The predominant menaquinone was identified as MK-8(H4ω-cycl). Mycolic acids were detected. The diagnostic phospholipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The predominant cellular fatty acids were identified as C16:0, C18:0, C18:1ω9c, 10-methyl C18:0 [tuberculostearic acid (TBSA)] and summed feature 3 (C16:1ω7c/C16:1ω6c). The G+C content of the genomic DNA was determined to be 71.4 mol%. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the strain from its most closely related strains. Based on morphological, chemotaxonomic and phylogenetic data, strain KLBMP S0043T is considered to represent a novel species of the genus Nocardia, for which the name Nocardia rhizosphaerae sp. nov. is proposed. The type strain is KLBMP S0043T (=CGMCC 4.7204 T = KCTC 29678T).

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

Access this article

Log in via an institution

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

References

  • Becker B, Lechevalier MP, Gordon RE, Lechevalier HA (1964) Rapid differentiation between Nocardia and Streptomyces by paper chromatography of whole-cell hydrolysates. J Appl Microbiol 12:421–423

    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 

  • Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    Article  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 39:783–789

    Article  Google Scholar 

  • Golinska P, Wang D, Goodfellow M (2013) Nocardia aciditolerans sp. nov., isolated from a spruce forest soil. Antonie Van Leeuwenhoek 103(5):1079–1088

    Article  PubMed Central  PubMed  Google Scholar 

  • Goodfellow M, Jones AL (2012) Order V. Corynebacteriales ord. nov. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn. Springer, New York, pp 232–243

    Chapter  Google Scholar 

  • Goodfellow M, Lechevalier MP (1989) Genus Nocardia Trevisan 1889, 9AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2348–2361

    Google Scholar 

  • Goodfellow M, Maldonado LA (2012) Genus I. Nocardia Trevisan 1889AL. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn. Springer, New York, pp 376–419

    Chapter  Google Scholar 

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

    Article  Google Scholar 

  • Groth I, Schumann P, Rainey FA, Martin K, Schuetze B, Augsten K (1997) Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 47:1129–1133

    Article  CAS  PubMed  Google Scholar 

  • He L, Li W, Huang Y, Wang L, Liu ZH (2005) Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 55:939–944

    Article  Google Scholar 

  • Kaewkla O, Franco CMM (2010) Nocardia callitridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree. Int J Syst Evol Microbiol 60:1532–1536

    Article  CAS  PubMed  Google Scholar 

  • Kelly KL, Judd DB (1976) Color. Universal language and dictionary of names (National Bureau of Standards special publication 440). US Department of Commerce, Washington, DC

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  • Kurup PV, Schmitt JA (1973) Numerical taxonomy of Nocardia. Can J Microbiol 19:1035–1048

    Article  CAS  PubMed  Google Scholar 

  • Lasker BA, Bell M, Klenk HP, Spröer C, Schumann C, Schumann P, Brown JM (2014) Nocardia vulneris sp. nov., isolated from wounds of human patients in North America. Antonie Van Leeuwenhoek 106(3):543–553

    Article  PubMed  Google Scholar 

  • Lechevalier MP, Lechevalier HA (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 34:435–444

    Article  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  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 

  • Minnikin 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  CAS  Google Scholar 

  • Qin S, Li J, Chen HH, Zhao GZ, Zhu WY, Jiang CL, Xu LH, Li WJ (2009) Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 75:6176–6186

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Qin S, Chen HH, Zhao GZ, Li J, Zhu WY, Xu LH, Jiang JH, Li WJ (2012) Abundant and diverse endophytic actinobacteria associated with medicinal plant Maytenus austroyunnanensis in Xishuangbanna tropical rainforest revealed by culture-dependent and culture-independent methods. Environ Microbiol Rep 4(5):522–531

    Article  PubMed  Google Scholar 

  • Saintpierre-Bonaccio D, Maldonado LA, Amir H, Pineau R, Goodfellow M (2004) Nocardia neocaledoniensis sp. nov., a novel actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil. Int J Syst Evol Microbiol 54(2):599–603

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Sazak A, Sahin N, Camas M (2012) Nocardia goodfellowii sp. nov. and Nocardia thraciensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 62:1228–1234

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Uchida K, Kudo T, Suzuki KI, Nakase T (1999) A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 45:49–56

    Article  CAS  PubMed  Google Scholar 

  • Vaddavalli R, Peddi S, Kothagauni SY, Linga VR (2014) Nocardia bhagyanesis sp. nov., a novel actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis), India. Antonie Van Leeuwenhoek 105(3):443–450

    Article  CAS  PubMed  Google Scholar 

  • Waksman SA (1961) Classification, identification, and descriptions of genera and species. The actinomycetes, vol 2. Williams & Wilkins, Baltimore, pp 331–332

    Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2452–2492

    Google Scholar 

  • Xing K, Qin S, Fei SM, Lin Q, Bian GK, Miao Q, Wang Y, Cao CL, Tang SK, Jiang JH, Li WJ (2011) Nocardia endophytica sp. nov., an endophytic actinomycete isolated from the oil-seed plant Jatropha curcas L. Int J Syst Evol Microbiol 61(8):1854–1858

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors are grateful to Prof. Iain C. Sutcliffe and two anonymous reviewers for their kind suggestions for improving this paper. This work was supported by Grants from the National Natural Science Foundation of China (No. 31370062, 31000005, 31170605), the opening project of the State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences (No. SKLMR-20130601), the Qing Lan Project of Jiangsu Province (2014), and the Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Author notes

    Authors and Affiliations

    1. The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, People’s Republic of China

      Yu Wang, Wei-Wei Feng, Xiao-Qi Zhou, Juan-Luan Bai, Bo Yuan, Xiu-Yun Ju, Cheng-Liang Cao, Ji-Hong Jiang, Ai-Jun Lv & Sheng Qin

    2. Department of Pediatrics, Anyang Children’s Hospital, Anyang, 455000, People’s Republic of China

      Wei Liu

    3. State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China

      Ying Huang

    Authors
    1. Yu Wang
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Wei Liu
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Wei-Wei Feng
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Xiao-Qi Zhou
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Juan-Luan Bai
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Bo Yuan
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Xiu-Yun Ju
      View author publications

      You can also search for this author in PubMed Google Scholar

    8. Cheng-Liang Cao
      View author publications

      You can also search for this author in PubMed Google Scholar

    9. Ying Huang
      View author publications

      You can also search for this author in PubMed Google Scholar

    10. Ji-Hong Jiang
      View author publications

      You can also search for this author in PubMed Google Scholar

    11. Ai-Jun Lv
      View author publications

      You can also search for this author in PubMed Google Scholar

    12. Sheng Qin
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Sheng Qin.

    Additional information

    Yu Wang and Wei Liu have contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary material 1 (DOCX 566 kb)

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Wang, Y., Liu, W., Feng, WW. et al. Nocardia rhizosphaerae sp. nov., a novel actinomycete isolated from the coastal rhizosphere of Artemisia Linn., China. Antonie van Leeuwenhoek 108, 31–39 (2015). https://doi.org/10.1007/s10482-015-0460-0

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s10482-015-0460-0

    Keywords

    Search

    Navigation