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Endophytes and Secondary Metabolites pp 249–267Cite as

Unraveling Plant-Endophyte Interactions: An Omics Insight

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Part of the book series: Reference Series in Phytochemistry ((RSP))

Abstract

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.

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Abbreviations

BLAST:

Basic local alignment search tool

BLAT:

BLAST-like alignment tool

Bp:

Base pairs

Brenda:

Braunschweig enzyme database

CAMERA:

Community cyberinfrastructure for advanced microbial ecology research and analysis

COGs:

Clusters of orthologous groups

DGGE:

Denaturing gradient gel electrophoresis

Gbp:

Giga base pairs

ITS:

Intertranscribing regions

KEGG:

Kyoto encyclopedia of genes and genomes

LSU:

Large subunit

LTQ:

Linear trap quadrupole

MALDI:

Matrix-assisted laser desorption/ionization

MALDI ToF:

Matrix-assisted laser desorption/ionization time of flight

Mbp:

Mega base pair

MEGAN:

MEtaGenome ANalyzer

MetAMOS:

Open source and modular metagenomic assembly and analysis pipeline

MG-RAST:

Metagenomic rapid annotations using subsystems technology

MS:

Mass spectroscopy

NCBI:

National center for biotechnology information

NGS:

Next-generation sequencing

NOGs:

Non-supervised orthologous groups

NR:

Negative regulatory domain

Pfam:

Protein families

PICRUSt:

Phylogenetic investigation of communities by reconstruction of unobserved states

PRINTS:

Protein fingerprints

Q-ToF:

Quadruple time-of-flight mass spectrometer

RDP:

Ribosomal database project

SMART:

Simple modular architecture research tool

SRTINGS:

Search tool for the retrieval of interacting genes/proteins

SSU:

Small subunit

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Acknowledgments

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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Authors and Affiliations

  1. Centre for Biotechnology, Siksha O Anusandhan University, Bhubaneswar, India

    Enketeswara Subudhi, Rajesh Kumar Sahoo, Suchanda Dey, Aradhana Das & Kalpana Sahoo

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  1. Enketeswara Subudhi
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  2. Rajesh Kumar Sahoo
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  3. Suchanda Dey
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  4. Aradhana Das
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Correspondence to Enketeswara Subudhi .

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Editors and Affiliations

  1. Department of Botany, University of Calcutta, Kolkata, West Bengal, India

    Sumita Jha

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Subudhi, E., Sahoo, R.K., Dey, S., Das, A., Sahoo, K. (2019). Unraveling Plant-Endophyte Interactions: An Omics Insight. In: Jha, S. (eds) Endophytes and Secondary Metabolites. Reference Series in Phytochemistry. Springer, Cham. https://doi.org/10.1007/978-3-319-90484-9_2

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