Microbial Ecology

, Volume 77, Issue 3, pp 676–688 | Cite as

Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities

  • B. S. Manjunatha
  • Sangeeta PaulEmail author
  • Chetana Aggarwal
  • S. Bandeppa
  • V. Govindasamy
  • Ajinath S. Dukare
  • Maheshwar S. Rathi
  • C. T. Satyavathi
  • K. Annapurna
Plant Microbe Interactions


Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.


Diversity Osmotolerant Genotype specificity Tissue specificity Bacillus sp. Functional characterization 



First author is thankful to the Indian Agricultural Research Institute, New Delhi, for providing the infrastructure facilities to carry out the research.

Funding Information

The first author is also thankful to the Indian Council of Agricultural Research for financial support in the form of fellowship.

Supplementary material

248_2018_1257_MOESM1_ESM.docx (12 kb)
Suppl. Fig 1 (DOCX 12 kb)
248_2018_1257_MOESM2_ESM.docx (12 kb)
Suppl. Table 1 (DOCX 12 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • B. S. Manjunatha
    • 1
  • Sangeeta Paul
    • 1
    Email author
  • Chetana Aggarwal
    • 2
  • S. Bandeppa
    • 3
  • V. Govindasamy
    • 1
  • Ajinath S. Dukare
    • 4
  • Maheshwar S. Rathi
    • 1
  • C. T. Satyavathi
    • 5
  • K. Annapurna
    • 1
  1. 1.Division of MicrobiologyICAR-Indian Agricultural Research InstituteNew DelhiIndia
  2. 2.ICAR-National Research Centre on Plant BiotechnologyNew DelhiIndia
  3. 3.Division of Soil ScienceICAR-Indian Institute of Rice ResearchHyderabadIndia
  4. 4.Division of Horticultural Crop ProcessingICAR-Central Institute of Post Harvest Engineering and TechnologyAboharIndia
  5. 5.ICAR-All India Coordinated Research Project on Pearl MilletJodhpurIndia

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