Organic Agriculture

, Volume 9, Issue 3, pp 331–343 | Cite as

Phenotypic and molecular characterization of diazotrophic bacteria associated with sugarcane in Bangladesh

  • Imam Taskin Alam
  • Syeda Roufun Nesa
  • Khandakar Mohiul Alam
  • Anowara Begum
  • Humaira AkhterEmail author


The study was conducted with the intent to isolate and characterize endophytic and diazotrophic bacteria from stem and roots of sugarcane (Saccharum sp.) and from associated rhizosphere with a wider goal to develop bio-fertilizer. Twenty-one samples of bacteria were isolated from sugarcane samples obtained from the test field of Bangladesh Sugarcane Research Institute (BSRI), Pabna, and from cultivation field of Ruppur, Bangladesh. Out of 21 isolates, 11 were identified as members of the class Gammaproteobacteria (with one exception) and majority of them were Enterobacteriaceae. The isolates were characterized by determining their metabolic characteristics, stress factor tolerance, plant growth-promoting attributes, and molecular characteristics. The isolates were phenotypically diverse, retaining some characteristics of Enterobacteriaceae. A significant number of isolates produced indole acetic acid and iron-chelator siderophore. Majority of them also solubilized phosphorus. Among molecular characteristics, the nifH gene region of Enterobacteriaceae family was detected by PCR amplification. The PCR products of 16S rRNA and nifH gene of representative isolates were sequenced and phylogenetically analyzed. This study establishes that a significant percentage of the bacteria found in the sugarcane stem, root, and associated rhizosphere has the potential to fix atmospheric nitrogen and promote plant growth. Therefore, they may have the feasibility to be used as bio-fertilizer.


Endophytes Diazotrophs Phenotypic Molecular Sequencing Phylogenetic 



The authors would like to thank Bioneer Sequencing Service, Korea ( for DNA sequencing.

Author’s contributions

KMA conceived the idea and provided samples for the experiment. ITA designed the experiments and carried it out with SRN. ITA analyzed data and interpreted the results. ITA wrote the manuscript with support from AB and HA. HA supervised the project. All authors read and approved the final manuscript.


This work was supported by the grant provided by the Ministry of Science and Technology, People’s Republic of Bangladesh, and University Grants Commission, Bangladesh.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interests.


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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Imam Taskin Alam
    • 1
  • Syeda Roufun Nesa
    • 1
  • Khandakar Mohiul Alam
    • 2
  • Anowara Begum
    • 1
  • Humaira Akhter
    • 1
    Email author
  1. 1.Department of MicrobiologyUniversity of DhakaDhakaBangladesh
  2. 2.Bangladesh Sugarcrop Research InstituteSoils and Nutrition DivisionPabnaBangladesh

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