Unraveling Plant-Endophyte Interactions: An Omics Insight

  • Enketeswara SubudhiEmail author
  • Rajesh Kumar Sahoo
  • Suchanda Dey
  • Aradhana Das
  • Kalpana Sahoo
Reference work entry
Part of the Reference Series in Phytochemistry book series (RSP)


Plants are home to a wide assemblage of nonpathogenic microbial community belonging to different phyla, bacteria, fungi, actinomycetes and viruses, the collective term for which is called endophyte. These endosymbiotic individuals exhibit endophytism principally by assisting in vigor and endurance to host plant and protect them from biotic (pathogenic infections) and abiotic stress (water, heat, nutrient, salinity, and herbivory). In return, these endosymbionts receive energy in the form of carbon from the host tissue. Colonization of endophyte in the internal tissues has been reported almost in every plant examined so far either in intercellular or intracellular mode. The form of relationships established with the host plant may be mutualistic, symbiotic, commensalistic, and trophobiotic. These are either rhizospheric or phyllospheric in origin. To establish such mutualistic relationships between plants and endophytes, certain chemical signals play important role in inducing production of the enhanced amount of secondary metabolites in host plant tissues. These novel metabolites act as a very good source of stress relievers to host and protect from grazing animals. The renewed interest in endophyte is due to the biotechnological relevance of these signal molecules as these have been used as a good source for production of biochemical compounds of industrial importance more specifically in agriculture and medicine. Additionally, their capacity to decontaminate soil bacteria and bring in soil fertility invites huge application in phytoremediation. However, the physiology, biochemistry, and genetics behind such complex interactions, exchange of chemical signals, and their production (the endophytism of plan-microbiome) are still half-understood. With the advent of new efficient analytical technology in molecular biology and genomics, the basic information on the existing diversity, phylogenetic lineage, evolution, and ecophysiological information about these endophytes has been tried to understand. However, the functional gene expression, posttranslational modifications, and protein turnover under various environmental circumstances are only revealed through transcriptome and proteomics analysis. Soon, high-throughput next-generation sequencing technology has remarkably changed the whole scenario of solving the intricate issues entangled with the complexity underlying endophytism. Sequencing of the whole genome of individuals following cultivable method (genomics), multiple host plants and their microbiome (comparative genomics), non-cultivable methods (metagenomics and metatranscriptomics), and microarray has been proved to be potential approaches to unravel the truth behind the plant-endophyte interactions. The present script deals with scopes, prospects, and outcomes of use of these “omics tools” to understand the deep insight into the mechanism of plant host infestation, biological reason behind the mutualism between host and endophytes, exchange of biochemical compounds, enhanced production of secondary metabolite, and host plant ecology.


Endophytes Genomics Metagenomics Metatranscriptomics Metaproteogenomics Endophytism 



Basic local alignment search tool


BLAST-like alignment tool


Base pairs


Braunschweig enzyme database


Community cyberinfrastructure for advanced microbial ecology research and analysis


Clusters of orthologous groups


Denaturing gradient gel electrophoresis


Giga base pairs


Intertranscribing regions


Kyoto encyclopedia of genes and genomes


Large subunit


Linear trap quadrupole


Matrix-assisted laser desorption/ionization


Matrix-assisted laser desorption/ionization time of flight


Mega base pair


MEtaGenome ANalyzer


Open source and modular metagenomic assembly and analysis pipeline


Metagenomic rapid annotations using subsystems technology


Mass spectroscopy


National center for biotechnology information


Next-generation sequencing


Non-supervised orthologous groups


Negative regulatory domain


Protein families


Phylogenetic investigation of communities by reconstruction of unobserved states


Protein fingerprints


Quadruple time-of-flight mass spectrometer


Ribosomal database project


Simple modular architecture research tool


Search tool for the retrieval of interacting genes/proteins


Small subunit



We gratefully acknowledge the infrastructure and support provided by Siksha O Anusandhan University, deemed to be university located at Bhubaneswar, for completing this work.


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Enketeswara Subudhi
    • 1
    Email author
  • Rajesh Kumar Sahoo
    • 1
  • Suchanda Dey
    • 1
  • Aradhana Das
    • 1
  • Kalpana Sahoo
    • 1
  1. 1.Centre for BiotechnologySiksha O Anusandhan UniversityBhubaneswarIndia

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