Rhizosphere Metagenomics: Methods and Challenges

Abstract

“Rhizosphere” is a narrow region associated with plant roots, acting as a residing place for millions of microorganisms. The rhizosphere-associated microbes are collectively called as root microbiome or rhizobiome. These microbiomes play a vital role in plant health by manipulating their growth and development. Rhizobiomes include both beneficial communities which enhance plant growth and improve plant defense mechanisms and pathogens which are harmful to plants. Nevertheless, the beneficial communities compete with the pathogens and colonize the roots. Though the significance of rhizosphere microbial community is well acknowledged, characterization of a plenty of microbes colonizing the rhizosphere is not done. Studying the rhizobiome of a crop species is an essential factor of crop improvement. “Metagenomics” is a frontier science that deals with study of metagenomes found in an environment such as rhizosphere. In this chapter, we have reviewed the most important metagenomic approaches and attributes to study the microbial diversity in the rhizosphere. We have discussed about the methods and software programs available for metagenome assembly, binning strategies, taxonomic classification, and functional annotation of metagenomics datasets. In addition, we have briefly pointed out the bottlenecks of the metagenomics approaches in studying the rhizobiomes.