Metagenome of rhizosphere and endophytic ecosystem

Abstract

Microbes inhabit almost every comer of earth with highest known to be in soil. The diversity and activity of microbes have been found to be high in plants (as endophytes) and the surrounding ecosystem (rhizosphere). Within plant, the roots seem to harbour more diverse microbes than any other part. Among other parameters, plant species and its age drive the define distinctness of microbial communities within plant and in soil. In addition, soil type and its management also influence the microbial diversity. These microbes produce various compounds that influence plant growth, productivity, susceptibility and resistance to biotic and abiotic stresses. Hence, structural and functional analysis of microbial communities associated with plant is very much essential to understand the various processes that define their functions. Culture-based analysis of all existing microbes is difficult largely due to limited knowledge of their culture requirements in laboratory. Molecular finger printing and high throughput sequencing of DNA isolated directly from the niches have proved to be an effective alternative to culture-based analysis. In recent past, much of the metagenomics work has been dedicated to study soil microbes, but limited information is available regarding the endophytic microbes. The information obtained by culture- independent analysis of soil microbes can help understand interaction between plant, soil and resident microbes. This is expected to pave the way for effective modulation of soil biological processes by rhizosphere engineering. Endophytic bacteria have been shown to have several beneficial effects on their host plant. Hence, further improvement in crop protection, production and soil health can be achieved by modulating plant's own processes through amending rhizospheric and endophytic microbes.