Metagenome sequencing of fingermillet-associated microbial consortia provides insights into structural and functional diversity of endophytes


Endophytes confer unique ecological advantages to their host plants. In this study, we have characterized the diversity of endophytic consortia associated with the GPU-28 (GPU) and Udurumallige (UM) finger millet varieties, which are resistant and susceptible to the blast disease, respectively. Whole genome metagenome sequencing of GPU and UM helped to identify 1029 species (includes obligate endophytes) of microbiota. Among them, 385 and 357 species were unique to GPU and UM, respectively. Remaining 287 species were common to both the varieties. Actinobacteria and other plant-growth promoting bacteria were abundant in GPU as compared to UM. Functional annotation of genes predicted from genomes of endophytes associated with GPU variety showed that many genes had functional role in stress response, secondary metabolism, aromatic compounds, glutathione, and cysteine synthesis pathways as compared to UM. Based on in vitro and in planta studies, Bacillus cereus and Paenibacillus spp. were found to be effective in suppressing the growth of blast disease pathogen Magnaporthe grisea (strain MG03). In the future, these strains could serve as potential biocontrol agents to reduce the incidence of blast disease in finger millet crop.

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Availability of sequenced data

The raw fastq files for the metagenome data were uploaded in NCBI SRA database with accession number SRP105033.


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HBM and MKP conceived and conceptualized the study. HBM and RUD collected the plant samples and isolated genomic DNA. RUD and KT performed the in vitro experiments. RCP analyzed the metagenome data. HBM guided metagenome data analysis. MEP assisted in maintaining cultures of endophytes and sequencing. HBM, MKP and BK wrote the manuscript. HBM, KSN and GVB edited the manuscript. KSN, KB and BP contributed in preparing the figures. All authors read and approved the final manuscript for publication.

Correspondence to M. K. Prasannakumar or H. B. Mahesh.

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Author Rajadurai, R. C. was employed by company AgriGenome Laboratory. All other authors declare no competing interests.

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Prasannakumar, M.K., Mahesh, H.B., Desai, R.U. et al. Metagenome sequencing of fingermillet-associated microbial consortia provides insights into structural and functional diversity of endophytes. 3 Biotech 10, 15 (2020) doi:10.1007/s13205-019-2013-0

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  • Endophytes
  • Metagenome sequencing
  • Blast disease
  • Magnaporthe
  • Fingermillet