A Metagenomic Approach to Identify Distinct Rhizospheric and Endophytic Bacterial Communities from Roots and Root Nodules of Vigna radiata

Abstract

Soil microbial community encompasses a perplexing range of physiological, metabolic and genomic diversity which can be explored through direct cultivation-based techniques or indirect molecular approaches. As cultivation-based methods are limited to only the culturable microorganisms, information about the majority of the unculturable diversity is missing. To circumvent this problem, molecular approaches based on the analysis of total DNA isolated from the environmental samples, often termed as metagenomic DNA, are employed. These molecular approaches can study the rare bacterial populations present in low abundance in soil. Though molecular approaches can study the soil diversity much better than the traditional culturable approaches, the success of any metagenomic study depends on the quality and quantity of DNA isolated from the metagenomic sample. In this chapter, metagenomic approaches have been employed to study the diversity of rhizospheric, root endophytic and root nodule bacterial communities of Vigna radiata. Results indicated that in rhizospheric and root nodule bacterial communities, Proteobacteria were predominant while in root endophytic communities, Actinobacteria were predominant. Deltaproteobacteria predominated rhizospheric community, whereas Gammaproteobacteria and Alphaproteobacteria dominated root endophytic and root nodule communities, respectively. Coupling traditional approaches with advanced next-generation sequencing techniques for accessing bacterial community ecology and physiology may bring new insights in understanding the microbial life in the rhizosphere and their further progression as root or nodule endophytes.