Isolation and characterization of growth-promoting bacteria from rhizosphere of Thymus danenensis and study of their potential for enhancement of seed germination

Document Type : Research Paper


1 Former Ph. D. Student, Department of Agronomy and Plant Breeding, University College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

2 Assistant Professor, Department of Agronomy and Plant Breeding, University College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

3 Assistant Professor, Medicinal Plants & Drug Research Institute, Shahid Beheshti University, Tehran, Iran

4 Professor, Department of Agronomy and Plant Breeding, University College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

5 Assistant Professor, Soil Science Department, University College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran


The Iranian Thymus daenensis subsp. daenensis is rich in monoterpene phenols (especially thymol and carvacrol). This research was conducted to isolate and characterize the plant growth promoting rhizobacteria (PGPRs) from rhizosphere of T. daenensis. PGPRs were screened based on some physiological traits including IAA production, phosphate solubilization, and siderophore compounds production abilities, and also seed germination and vigor tests. Twenty one rhizobacteria were isolated from the rhizosphere samples of T. daenensis which grow widely in Iran, and their effect on seed germination properties was studied in a completely randomized block design with three replications. We could characterize four isolates for PGPRs activity based on physiological and germination assays. TDE3, TDE16 and TDE20 isolates had the phosphate solubilization and siderophores production abilities. TDE4 (Achromobacter spiritinus) was the only isolated bacteria which significantly improved the SGR and VI of T. daenensis seeds. These four isolates have the potential to be used as PGPRs in cultivation of T. daenensis.


  1. Abdul Baki, A.A. & Anderson, J.D. (1973). Vigor determination in soybean seed by multiple criteria. Crop Science, 13, 630-633.
  2. Alexander, D. B. & Zuberrer, D. A. (1991). Use of chrome azurol S reagent to evaluate siderophore production by rhizobacteria. Biology and Fertility of Soil, 12(1), 39-45.
  3. Ashrafuzzaman, M., Hossen, F.A., Razi Ismail, M., Anamul Hoque, M.D. & Zahurul Islam, M. et al. (2009). Efficiency of plant growth-promoting rhizobacteria (PGPR) for the enhancement of rice growth. African Journal of Biotechnology, 8(7), 1247-1252.
  4. Barazani, O. & Friedman, J. (1999). Is IAA the major root growth factor secreted from plant-growth mediating bacteria? Journal of Chemical Ecology, 25(10), 2397-2406.
  5. Baset Mia, M.A., Shamsuddin, Z.H. & Mahmood, M. (2012). Effects of rhizobia and plant growth promoting bacteria inoculation on germination and seedling vigor of lowland rice. African Journal of Biotechnology, 11(16), 3758-3765.
  6. Bric, J.M., Bustock, R.M. & Silversone, S.E. (1991). Rapid in situ assay for indole acetic acid production by bacterial immobilization on a nitrocellulose membrane. Applied and Environmental Microbiology, 57, 535-538.
  7. Claus, D. & Berkely, R. (1986). Genus Bacillus. In Bergey’s manual of systematic bacteriology, ed. by Williams, S.T., Sharp, M.E., and Holt, J.C., Williams and Wilkins, Baltimor MD 21202, pp. 1105-1139.
  8. De Bellis, P. & Ercolani, G.L. (2001). Growth Interactions during bacterial colonization of seedling rootlets. Applied and Environmental Microbiology, 67(4), 1945-1948.
  9. Desai, S., Narayanaiah, C.h., Kranti Kumari, C.h., Reddy, M.S., Gnanamanickam, S.S. et al. (2007). Seed inoculation with Bacillus sp. improves seedling vigour in oil-seed plant Jatropha curcas L. Biology and Fertility of Soils, 44, 229-234.
  10. Devlin, R.M. (1969). Plant physiology: Second edition. Reinhold Publishing Corporation, New York.
  11. Elo, S., Maunuksela, L., Salkinoja-Salonen, M., Smolander, A. & Haahtela, K. (2000). Humus bacteria of Norway spruce stands: plant growth promoting properties and birch, red fescue and alder colonizing capacity. FEMS Microbiology and Ecology, 31, 143-152.
  12. Glickmann, E. & Dessaux, Y. (1995). A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Applied and Environmental Microbiology, 61, 793-796.
  13. Guerinot, M.L. (1994). Microbial iron transport. Annual Review of Microbiology, 48, 743-772.
  14. Höfte, M. (1993). Classes of microbial siderophores. In Iron chelation in plants and soil microorganisms, ed. by Barton, L.L., and Hemming, B.C. Academic Press, San Diego, California, pp. 3-26.
  15. International Seed Testing Association. (1985). International rules for seed testing. Seed Science and Technology, 13, Supplement, pp. 307.
  16. Jacobson, C.B., Pasternak, J.J. & Glick, B.R. (1994). Partial purification and characterization of 1-aminocyclopropane-1-carboxylate deaminase from the plant growth promoting rhizobacterium Pseudomonas putida GR12-2. Canadian Journal of Microbiology, 40, 1019-1025.
  17. Kende, H. (1993). Ethylene biosynthesis. Annual Review of Plant Physiology and Plant Molecular Biology, 33, 172-296.
  18. Khalid, A., Arshad, M. & Zahir, Z.A. (2004). Screening plant growth promoting rhizobacteria for improving growth and yield of wheat. Journal of Applied Microbiology, 96, 473-480.
  19. Kochar, M., Upadhyay, A. & Srivastava, S. (2011). Indole-3-acetic acid biosynthesis in the biocontrol strain Pseudomonas fluorescens Psd and plant growth regulation by hormone overexpression. Research in Microbiology, 162, 426-435.
  20. Kucey, R.M.N., Janzen, H.H. & Leggett, M.E. (1989). Microbially mediated increases in plant available phosphorus. In Advances in Agronomy, ed. by Brady N.C. Academic Press INC, San Diego, California, 42, pp. 199-223.
  21. Maguire, J.D. (1962). Speed of germination- aid in selection and evaluation for seedling emergence and vigor. Crop Science, 2, 176-177.
  22. Mirza, M.S., Ahmad, W., Latif, F., Haurat, J. & Bally, R. et al. (2001). Isolation, partial characterization, and the effect of plant growth-promoting bacteria (PGPB) on micro-propagated sugarcane in vitro. Plant Soil, 237, 47-54.
  23. Moeinzadeh, A., Sharif-Zadeh, F., Ahmadzadeh, M. & Heidari Tajabadi, F. (2010). Biopriming of sunflower (Helianthus annuus L.) seed with Pseudomonas fluorescens for improvement of seed invigoration and seedling growth. Australian Journal of Crop Sciences, 4(7), 564-570.
  24. Nikavar, B., Mojab, F. & Dolat Abadi, R. (2005). Analysis of the essential oils of two Thymus species from Iran.  Food Chemistry, 90, 609-611.
  25. Patten, C.L. & Glick, B.R. (2002). Role of Pseudomonas putida indoleacetic acid in development of the host plant root system. Applied and Environmental Microbiology, 68(8), 3795-3801.
  26. Patten, C.L. & Glick, B.R. (1996). Bacterial biosynthesis of indole-2-acetic acid. Canadian Journal of Microbiology, 31, 196-119.
  27. Pikovaskya, R.I. (1948). Mobilization of phosphorus in soil in connection with the vital activity of some microbial species. Mikrobiologiya, 17, 362-370.
  28. Rana, A., Saharan, B., Joshi, M., Prasanna, R., Kumar, K. et al. (2011). Identification of multi-trait PGPR isolates and evaluating their potential as inoculants for wheat. Annals of Microbiol, 61(4), 893-900.
  29. Rechinger, K.H. (1982). Flora Iranica (Vol. 152). Graz: Akademische Druck- und Verlagsanstalt, University of Chicago.
  30. Sajjadi, S.E. & Khatamsaz, M. (2003). Composition of the essential oil of Thymus daenensis Celak. ssp lancifolius (Celak.) Jalas. Journal of Essential Oil Reserch, 15, 34-35.
  31. SAS. (2006). Version 9.0. SAS/STAT. Guide to Personal Computers. SAS Institute Inc, Cary, North Carolina.
  32. Schwyn, B. & Neilands, J.B. (1987). Universal chemical assay for the detection and determination of siderophores. Analytical Biochemistry, 160, 47-56.
  33. Stahl-Biskup, E. & Saez, F. (2003). Thyme, second ed., Taylor & Francis, London.
  34. Tilak, K.V.B.R., Ranganayaki, N. et al. (2005). Diversity of plant growth and soil health supporting bacteria. Current Science, 89(1), 136-150.
  35. Vessey, J.K. (2003). Plant growth promoting rhizobacteria as biofertilizers. Plant Soil, 255, 571-586.
  36. Vincent, J.M. (1970). A manual for the practical study of root-nodule bacteria. Blackwell Scientific Publication, Oxford, UK.
  37. Wu, S.C., Cao, Z.H., Li, Z.G., Cheung, K.C. & Wong, M.H. (2005). Effects of biofertilizer containing N-fixer, P and K solubilizers and AM fungi on maize growth: a greenhouse trial. Geoderma, 125, 155-166.
  38. Xie, H., Pasternak, J.J. & Glick, B.R. (1996). Isolation and characterization of mutants of the plant growth-promoting rhizobacterium Pseudomonas putida GR12-2 that overproduce indoleacetic acid. Current Microbiology, 21, 56-60.