Skip to main content
SpringerLink
Log in

Actinomadura hankyongense sp. nov. Isolated From Soil of Ginseng Cultivating Field

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

A Gram-positive, rod-shaped, non-spore-forming, and aerobic bacterium (Gsoil 556T) was isolated from soil of a ginseng field and subjected to its taxonomic position. Based on 16S rRNA gene sequence similarity, strain Gsoil 556T was shown to belong to the genus Actinomadura of the family Thermomonosporaceae and was closely related to A. montaniterrae CYP1-1BT (99.3%), A. nitritigenes DSM 44137T (98.7%), and A. rudentiformis HMC1T (98.5%), while it showed less than 98.4% sequence similarity to the other species of this genus. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that it is most closely related to A. rudentiformis HMC1T and A. nitritigenes DSM 44137T. The DNA G+C content was 73.1 mol%. The peptidoglycan was meso-diaminopimelic acid and the whole-cell sugar contained fucose, galactose, glucose, mannose, and ribose. The predominant menaquinone (KK) was MK-9(H8) [55%] and MK-9(H6) [45%]. The major cellular fatty acids were C14:0, C16:0, C18:1 ω9c and summed feature 3 (C16:1 ω6c/C16:1 ω7c). All these data supported the affiliation of strain Gsoil 556T to the genus Actinomadura. The DNA–DNA hybridization between strain Gsoil 556T and its phylogenetically closest relatives were less than 40%. Furthermore, the results of physiological and biochemical tests enabled strain Gsoil 556T to be differentiated genotypically and phenotypically from currently known Actinomadura species. Therefore, strain Gsoil 556T represents a novel species of the genus Actinomadura, for which the name Actinomadura hankyongense sp. nov. is proposed. The type strain Gsoil 556T (=KACC 19438T=LMG 30327T).

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

Similar content being viewed by others

References

  1. Atlas RM (1993) Handbook of microbiological media. CRC Press, Boca Raton

    Google Scholar 

  2. Buck JD (1982) Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    PubMed  CAS  PubMed Central  Google Scholar 

  3. Cappuccino JG, Sherman N (2002) Microbiology, a laboratory manual, 6th edn. Pearson Education, Inc., California

    Google Scholar 

  4. 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 

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

    Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

  7. Gauze GF, Terekhova LP, Galatenko OA, Preobrazhenskaya TP, Borisova VN, Federova GB (1987) Actinomadura cremea subsp. rifamicini subsp. nov. In validation of the publication of new names and new combinations previously effectively published outside the IJSB: list no. 23. Int J Syst Bacteriol 37:179–180

    Article  Google Scholar 

  8. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  9. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469

    Article  CAS  Google Scholar 

  10. Im WT, Liu QM, Yang JE, Kim MS, Kim SY, Lee ST, Yi TH (2010) Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field. J Microbiol 48:262–266

    Article  PubMed  Google Scholar 

  11. Kim MM, Siddiqi MZ, Im WT (2017) Mucilaginibacter ginsenosidivorans sp. nov., isolated from soil of Ginseng field. Curr Microbiol 74:1382–1388

    Article  PubMed  CAS  Google Scholar 

  12. Kimura M (1983) The neutral theory of molecular evolution. Cambridge Cambridge University Press, Cambridge

    Book  Google Scholar 

  13. Komagata K, Suzuki K (1987) Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–203

    Article  CAS  Google Scholar 

  14. Kroppenstedt RM, Goodfellow M (2006) The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillospora and Thermomonospora. In: Dworkin M, Falkow S, Rosenberg E (eds) The prokaryotes, vol 3, 3rd edn. Springer, KH Schleifer, pp 682–724

    Chapter  Google Scholar 

  15. Kroppenstedt RM, Stackebrandt E, Goodfellow M (1990) Taxonomic revision of the actinomycete genera Actinomadura and Microtetraspora. Syst Appl Microbiol 13:148–160

    Article  CAS  Google Scholar 

  16. Le RM, Meyers PR (2007) Actinomadura rudentiformis sp. nov., isolated from soil. Int J Syst Evol Microbiol 57:45–50

    Article  CAS  Google Scholar 

  17. Lechevalier HA, Lechevalier MP (1968) A critical evaluation of the genera of aerobic actinomycetes. In: Prauser H (ed) The actinomycetales. VEB Gustav Fischer Verlag, Jena, pp 393–405

    Google Scholar 

  18. Lipski A, Altendorf K (1995) Actinomadura nitritigenes sp. nov., isolated from experimental biofilters. Int J Syst Bacteriol 45:717–723

    Article  CAS  Google Scholar 

  19. Mertz FP, Yao RC (1990) Actinomadura fibrosa sp. nov. isolated from soil. Int J Syst Bacteriol 40:28–33

    Article  PubMed  CAS  Google Scholar 

  20. 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 

  21. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  22. Moore DD, Dowhan D (1995) Preparation and analysis of DNA. In: Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA (eds) Current protocols in molecular biology. Wiley, Struhl K New York, pp 2–11

    Google Scholar 

  23. Preobrazhenskaya TP, Lavrova NV, Ukholina RS, Nechaeva NP (1975) Isolation of new species of the genus Actinomadura on selective media with streptomycin and bruneomycin. Antibiotiki 20:404–409 (in Russian)

    Google Scholar 

  24. Promnuan Y, Kudo T, Ohkuma M, Chantawannakul P (2011) Actinomadura apis sp. nov., isolated from a honey bee (Apis mellifera) hive, and the reclassification of Actinomadura cremea subsp. 1987 as Actinomadura rifamycini (Gauze et al. 1987) sp. nov., comb. nov. Int J Syst Evol Microbiol 61:2271–2277

    Article  PubMed  CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    Google Scholar 

  27. Siddiqi MZ, Im WT (2016) Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 66:3449–3455

    Article  PubMed  CAS  Google Scholar 

  28. Siddiqi MZ, Im WT (2016) Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field. Arch Microbiol 198:551–557

    Article  PubMed  CAS  Google Scholar 

  29. Siddiqi MZ, Aslam Z, Im WT (2017) Arachidicoccus ginsenosidivorans sp. nov., with ginsenosideconverting activity isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 67:1005–1010

    Article  PubMed  Google Scholar 

  30. Siddiqi MZ, Lee SY, Choi KD, Im WT (2018) Aeromicrobium panacisoli sp. nov. isolated from soil of Ginseng. Curr Microbiol 75:624–629

    Article  PubMed  CAS  Google Scholar 

  31. Siddiqi MZ, Liu Q, Kang MS, Kim MS, Im WT (2016) Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng. Int J Syst Evol Microbiol 66:1125–1130

    Article  CAS  Google Scholar 

  32. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT (2016) Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 66:4039–4045

    Article  PubMed  CAS  Google Scholar 

  33. Siddiqi MZ, Muhammad Shafi S, Im WT (2017) Complete genome sequencing of Arachidicoccus ginsenosidimutans sp. nov., and its application for production of minor ginsenosides by finding a novel ginsenoside-transforming b-glucosidase. RSC Adv 7:46745

    Article  CAS  Google Scholar 

  34. Songsumanus A, Kudo T, Ohkuma M, Phongsopitanun W, anasupawat S (2016) Actinomadura montaniterrae sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 66:3310–3316

    Article  PubMed  CAS  Google Scholar 

  35. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  36. 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  PubMed  CAS  PubMed Central  Google Scholar 

  37. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al (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 

Download references

Acknowledgements

This research was supported by the project on survey and excavation of Korean indigenous species of the National Institute of Biological Resources (NIBR) under the Ministry of Environment and by the Intelligent Synthetic Biology Center of Global Frontier Project funded by the Ministry of Education, Science and Technology (2014M3A6A8066437) and this work was supported by the Intelligent Synthetic Biology Center of Global Frontier Project funded by the Ministry of Science and ICT (2011-0031955).

Author information

Authors and Affiliations

  1. Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea

    Muhammad Zubair Siddiqi, Soon Youl Lee & Wan Taek Im

  2. AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea

    Qingmei Liu

  3. Sellusone Co., Ltd., 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea

    Qingmei Liu, Kang Duk Choi & Wan Taek Im

  4. Department of Food & Nutrtion, Seoil University, Seoul, Republic of Korea

    Jae Hag Lee

Authors
  1. Muhammad Zubair Siddiqi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qingmei Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kang Duk Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Soon Youl Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jae Hag Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wan Taek Im
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wan Taek Im.

Additional information

The NCBI GenBank accession number for the 16S rRNA gene sequence of strain Gsoil 556T is KY078843.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 3329 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Siddiqi, M.Z., Liu, Q., Choi, K.D. et al. Actinomadura hankyongense sp. nov. Isolated From Soil of Ginseng Cultivating Field. Curr Microbiol 75, 1401–1407 (2018). https://doi.org/10.1007/s00284-018-1536-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-018-1536-7

Search

Navigation