Neem Microbiome

  • Varalaxmi B. Agasimundin
  • Kannan Rangiah
  • Ambardar Sheetal
  • Malali GowdaEmail author
Part of the Compendium of Plant Genomes book series (CPG)


Endophytes are the microorganisms that persist within or between tissues of plants without causing any negative effect on plant’s growth and development. Endophytes are mutually co-evolved with host plant species and have been reported to produce secondary metabolites similar to host plants. In this study, we developed unique neem-based media to isolate neem endophytic fungi and bacteria. A total of 361 fungi and 80 bacterial endophytes were isolated from various parts of neem plant including leaf, flower, seed, bark, cortex, and root using neem-based media. This is the first of its kind to demonstrate culturing of endophytic fungi and bacteria on a selective neem-based media without using any external nutrients. Out of total 376 fungal endophytes and 80 bacterial endophytes, only 10 fungi and 3 bacteria were inhibiting the growth of pathogenic rice blast fungi, Magnaporthe oryzae which were further identified using ITS and 16S rRNA sequencing. Finally, two fungal isolates identified as Fusarium sp.,st.Ai.67A and Neocosmospora ramose Ai.51D and two bacterial isolates identified as Pantoea sp. Ai.A2 and Bacillus sp. Ai.C5 were further selected for secondary metabolite production. These microbes were found to produce three neem metabolites such as Epoxy/hydroxyazadiradione, nimbin, and salanin. These endophytes will have great potential applications in agriculture, medicine, and bio-energy.


Endophytes Neem media 16S rRNA ITS Magnaporthe Metabolites 



We would like to thank Mahesh H B, Indira B.S, Shirke M, Yenagi V and Janani S for their help in endophytes isolation and DNA fingerprinting.


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Varalaxmi B. Agasimundin
    • 1
    • 2
  • Kannan Rangiah
    • 2
  • Ambardar Sheetal
    • 1
    • 2
  • Malali Gowda
    • 1
    • 2
    Email author
  1. 1.Centre for Functional Genomics and BioinformaticsTransDisciplinary UniversityBengaluruIndia
  2. 2.Centre for Cellular and Molecular PlatformsBengaluruIndia

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