Plant and Soil

, Volume 379, Issue 1–2, pp 51–66 | Cite as

Physiological and genetic characterization of rice nitrogen fixer PGPR isolated from rhizosphere soils of different crops

  • Safiullah Habibi
  • Salem Djedidi
  • Kunlayakorn Prongjunthuek
  • Md Firoz Mortuza
  • Naoko Ohkama-Ohtsu
  • Hitoshi Sekimoto
  • Tadashi YokoyomaEmail author
Regular Article



We aimed to identify plant growth-promoting rhizobacteria that could be used to develop a biofertilizer for rice.


To obtain plant growth-promoting rhizobacteria, rhizosphere soils from different crops (rice, wheat, oats, crabgrass, maize, ryegrass, and sweet potato) were inoculated to rice plants. In total, 166 different bacteria were isolated and their plant growth-promoting traits were evaluated in terms of colony morphology, indole-3-acetic acid production, acetylene reduction activity, and phosphate solubilization activity. Moreover, genetic analysis was carried out to evaluate their phylogenetic relationships based on 16S rRNA sequence data.


Strains of Bacillus altitudinis, Pseudomonas monteilii, and Pseudomonas mandelii formed associations with rice plants and fixed nitrogen. A strain of Rhizobium daejeonense showed nitrogen fixation activity in an in vitro assay and in vivo. Strains of B. altitudinis and R. daejeonense derived from rice rhizosphere soil, strains of P. monteilii and Enterobacter cloacae derived from wheat rhizosphere soil, and a strain of Bacillus pumilus derived from maize rhizosphere soil significantly promoted rice plant growth.


These methods are effective to identify candidate species that could be developed as biofertilizers for target crops.


Rhizosphere Plant growth promoting rhizobacteria Rice Nitrogen fixation IAA Phosphate solubilization 16S rRNA Bacillus altitudinis Pseudomonas monteilii Pseudomonas mandelii Rhizobium daejeonense 



Plant growth promoting rhizobacteria


Indole-3-acetic acid


Acetylene reduction assay


Deoxyribonucleic acid


Hexadecyltrimethylammonium bromide


Polymerase chain reaction


DNA data bank Japan


Basic local alignment search tool


Japan Atomic Energy Agency


Randomized block design



This study was supported by the Special Research Fund of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan titled “Research and development of security and safe crop production to reconstruct agricultural lands in Fukushima prefecture based on novel techniques to remove radioactive compounds using advanced bio-fertilizer and plant protection strategies”. This work was also supported by a Grant-in-Aid for Scientific Research (B):24380176 from the Japan Society for the Promotion of Science (JSPS).


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Safiullah Habibi
    • 1
  • Salem Djedidi
    • 2
  • Kunlayakorn Prongjunthuek
    • 3
  • Md Firoz Mortuza
    • 4
  • Naoko Ohkama-Ohtsu
    • 5
  • Hitoshi Sekimoto
    • 6
  • Tadashi Yokoyoma
    • 5
    Email author
  1. 1.United Graduate School of AgricultureTokyo University of Agriculture and TechnologyTokyoJapan
  2. 2.Faculty of AgricultureTokyo University of Agriculture and TechnologyTokyoJapan
  3. 3.Soil Microbiology Research Group, Soil Science Division, Department of AgricultureBangkokThailand
  4. 4.Institute of Food and Radiation BiologyBangladesh Atomic Energy CommissionDhakaBangladesh
  5. 5.Institute of AgricultureTokyo University of Agriculture and TechnologyTokyoJapan
  6. 6.Faculty of AgricultureUtsunomiya UniversityUtsunomiyaJapan

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