Skip to main content
SpringerLink
Log in

Microbacterium horti sp. nov., a bacterium isolated from Cucurbita maxima cultivating soil

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

A novel bacterial strain THG-SL1T was isolated from a soil sample of Cucurbita maxima garden and was characterized by using a polyphasic approach. Cells were Gram-reaction-positive, non-motile and rod-shaped. The strain was aerobic, catalase positive and weakly positive for oxidase. Phylogenetic analysis based on 16S rRNA gene sequence analysis but it shared highest similarity with Microbacterium ginsengisoli KCTC 19189T (96.6 %), indicating that strain THG-SL1T belongs to the genus Microbacterium. The DNA G + C content of the isolate was 68.9 mol %. The major fatty acids were anteiso-C15: 0 (39.7 %), anteiso-C17: 0 (24.4 %) and iso-C16: 0 (18.5 %). The major polar lipids of strain THG-SL1T were phosphatidylglycerol (PG) and an unidentified glycolipid (GL). The predominant respiratory isoprenoid quinones were menaquinone-11 and menaquinone-12. The diamino acid in the cell-wall peptidoglycan was ornithine. Based on the results of polyphasic characterization, strain THG-SL1T represented a novel species within the genus Microbacterium, for which the name Microbacterium horti sp. nov. is proposed. The type strain is THG-SL1T (=KACC 18286T=CCTCC AB 2015117T).

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

  • Alves A, Correia A, Igual JM, Trujillo ME (2014) Microbacterium endophyticum sp. nov. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium. Syst Appl Microbiol 37:474–479

    Article  PubMed  Google Scholar 

  • Anand S, Bala K, Saxena A, Schumann P, Lal R (2012) Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site. Int J Syst Evol Microbiol 62:2114–2120

    Article  CAS  PubMed  Google Scholar 

  • Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London, pp 267–287

    Google Scholar 

  • Collins MD, Bradbury JF (1992) The genera Agromyces, Aureobacterium, Clavibacter, Curtobacterium, and Microbacterium. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd edn. Springer, Berlin, pp 1355–1368

    Google Scholar 

  • Collins MD, Jones D, Kroppenstedt RM (1983) Reclassification of Brevibacterium imperiale (Steinhaus) and “Corynebacterium laevaniformans’’ (Dias and Bhat) in a Redefined Genus Microbacterium (Orla-Jensen), as Microbacterium imperiale comb. nov. and Microbacterium laevaniformans nom. rev.; comb. nov. Syst Appl Microbiol 4:65–78

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  • 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 

  • 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 

  • Kim KK, Lee KC, Oh HM, Lee JS (2008) Microbacterium aquimaris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 58:1616–1620

    Article  CAS  PubMed  Google Scholar 

  • Kim YJ, Kim MK, Bui TPN, Kim HB, Srinivasan S, Yang DC (2010) Microbacterium ginsengiterrae sp. nov., a β-glucosidase-producing bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 60:2808–2812

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park C, 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 

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

    Book  Google Scholar 

  • Kook M, Son H-M, Yi T-H (2014) Microbacterium kyungheense sp. nov. and Microbacterium jejuense sp. nov., isolated from salty soil. Int J Syst Evol Microbiol 64:2267–2273

    Article  CAS  PubMed  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acid Techniques in Bacterial Systematics. Wiley, Chichester, pp 115–175

    Google Scholar 

  • Liu J, Nakayama T, Hemmi H, Asano Y, Tsuruoka N, Shimomura K, Nishijima M, Nishino T (2005) Microbacterium natoriense sp. nov., a novel d-aminoacylase-producing bacterium isolated from soil in Natori Japan. Int J Syst Evol Microbiol 55:661–665

    Article  CAS  PubMed  Google Scholar 

  • Liu QM, Im WT, Lee M, Yang DC, Lee ST (2006) Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 56:1939–1944

    Article  CAS  PubMed  Google Scholar 

  • Madhaiyan M, Poonguzhali S, Lee J-S, Lee K-C, Saravanan VS, Santhanakrishnan P (2010) Microbacterium azadirachtae sp. nov., a plant-growth-promoting actinobacterium isolated from the rhizoplane of neemseedlings. Int J Syst Evol Microbiol 60:1687–1692

    Article  CAS  PubMed  Google Scholar 

  • Matsuyama H, Kawasaki K, Yumoto I, Shida O (1999) Microbacterium kitamiense sp. nov., a new polysaccharide-producing bacterium isolated from the wastewater of a sugar-beet factory. Int J Syst Bacteriol 49:1353–1357

    Article  PubMed  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, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117

    Article  CAS  Google Scholar 

  • Mondani L, Piette L, Christen R, Bachar D, Berthomieu C, Chapon V (2013) Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil. Int J Syst Evol Microbiol 63:2600–2606

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Orla-Jensen S (1919) The lactic acid bacteria. Host and Sons, Copenhagen

    Google Scholar 

  • Park HY, Kim KK, Jin L, Lee ST (2006) Microbacterium paludicola sp. nov., a novel xylanolytic bacterium isolated from swamp forest. Int J Syst Evol Microbiol 56:535–539

    Article  CAS  PubMed  Google Scholar 

  • Park MJ, Kim MK, Kim HB, Im WT, Yi TH, Kim SY, Soung NK, Yang DC (2008) Microbacterium ginsengisoli sp. nov., a β-glucosidase-producing bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 58:429–433

    Article  CAS  PubMed  Google Scholar 

  • 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 

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

  • Schippers A, Bosecker K, Spröer C, Schumann P (2005) Microbacterium oleivorans sp. nov. and Microbacterium hydrocarbonoxydans sp. nov., novel crude-oil-degrading Gram-positive bacteria. Int J Syst Evol Microbiol 55:655–660

    Article  CAS  PubMed  Google Scholar 

  • Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shivaji S, Bhadra B, Rao RS, Chaturvedi P, Pindi PK, Raghukumar C (2007) Microbacterium indicum sp. nov., isolated from a deep-sea sediment sample from the Chagos Trench, Indian Ocean. Int J Syst Evol Microbiol 57:1819–1822

    Article  CAS  PubMed  Google Scholar 

  • Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams and Wilkins, Baltimore

    Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849

    Article  CAS  Google Scholar 

  • Takahashi K, Nei M (2000) Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 17:1251–1258

    Article  CAS  PubMed  Google Scholar 

  • Takeuchi M, Hatano K et al (1998) Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium. Int J Syst Bacteriol 48:739–747

    Article  CAS  PubMed  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  PubMed Central  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 

  • Yokota A, Takeuchi M, Weiss N (1993) Proposal of two new species in the genus Microbacterium: microbacterium dextranolyticum sp. nov. and Microbacterium aurum sp. nov. Int J Syst Bacteriol 43:549–554

    Article  Google Scholar 

  • Zlamala C, Schumann P, Kämpfer P, Valens M, Rosselló-mora R, Lubitz W, Busse HJ (2002) Microbacterium aerolatum sp. nov., isolated from the air in the ‘Virgilkapelle’ in Vienna. Int J Syst Evol Microbiol 52:1229–1234

    CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was conducted under the industrial infrastructure program (No.N0000888) for fundamental technologies which is funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea).

Author information

Author notes

    Authors and Affiliations

    1. Department of Oriental Medicinal Material and Processing College of Life Science, Kyung Hee University, 1 Seocheon, Kihung Yongin, Kyunggi, 446-701, Republic of Korea

      Shahina Akter

    2. Graduate School of Biotechnology, Kyung Hee University, 1 Seocheon, Kihung Yongin, Kyunggi, 446-701, Republic of Korea

      Jae Hee Park

    3. Department of Acupuncture Meridian Science Research Center, College of Korean Medicine, Kyung Hee University, # 1 Hoegi-dong, Dongdaemun-gu, Seoul, 130-701, Republic of Korea

      Chang Shik Yin

    Authors
    1. Shahina Akter
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Jae Hee Park
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Chang Shik Yin
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Chang Shik Yin.

    Additional information

    Communicated by Erko Stackebrandt.

    Shahina Akter and Jae Hee Park have equally contributed to this work.

    The NCBI GenBank accession number for the 16S rRNA gene sequence of strain THG-SL1T is KM576855.

    Electronic supplementary material

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Akter, S., Park, J.H. & Yin, C.S. Microbacterium horti sp. nov., a bacterium isolated from Cucurbita maxima cultivating soil. Arch Microbiol 198, 233–240 (2016). https://doi.org/10.1007/s00203-015-1183-3

    Download citation

    • Received:

    • Revised:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s00203-015-1183-3

    Keywords

    Search

    Navigation