Metagenomic Approach in Relation to Plant–Microbe and Microbe–Microbe Interactions

Abstract

Metagenomics is the study of collective microbial genomes of environmental samples. Microorganisms are essential components of every part of life on the planet. Microorganisms do not exist as individuals, but they form complex communities (microbiomes) in the above-ground and below-ground parts of the plants, contributing to the plant’s growth, health, and performance in many ways. There are several factors that regulate the structure and composition of the microbes interacting with plants. However, it has been calculated that only 0.1% of the microbes found in the environment are culturable, and remaining are uncultivable and untapped. The unculturable microbial communities are referred to as “microbial dark matter” which almost covers a high percentage of the planet’s biomass and biodiversity. However, only very little is known about these microbiomes and their interactions with a host. Every microbial genome contains a unique set of genes encoding novel enzymes used for biotechnological applications. Metagenomics methods using advanced sequencing technologies enable tracking of these novel biological molecules that are available in the natural systems in a high-throughput manner. Metagenomics approach also unravels the microbial interactions between themselves and between plants and the microbes as well. This chapter describes the significance of microbial interactions and how plant–microbiome and microbe–microbe interactions are being studied by metagenomics approaches.