Deciphering the Rhizosphere Microbiome Through Metagenomics

The rhizosphere is the region of soil that is in immediate contact with the plant roots. The chemical composition of the root exudates defines the entire microbial community composition. A thorough metagenomic study is of immense significance, enabling a bird’s eye view into the whole rhizospheric micro-domain. Diversified populations of plant growth-promoting rhizobacteria exhibiting an indispensable role in mitigating stress responses to both biotic and abiotic stress have been deciphered by rhizosphere microbiome study. This chapter deals with the noteworthy role of metagenomics in unraveling the rhizosphere community composition, dynamic diversity, and its potential role in plant stress mitigation and bioprospecting. As a consequence of priming, the plant growth-promoting rhizobacterial population releases antagonistic agents such as VOCs, ACC deaminase, antibiotics, siderophores, LOCs, AHLs, and lipopolypeptides, which serve as defense priming agents against phytopathogenic fungi and bacteria thus exhibiting resistance to biotic agents. Metagenomics has helped elucidate the rhizosphere microbiome’s remarkable role in mitigating abiotic stress responses specifically heavy metals, salinity, chilling, iron deficiency chlorosis, and nitrogen deficiency. A deep insight into the genetic profile of the rhizosphere of stressed and non-stressed plants has revealed significant differences relating to the predominance of a few plant growth-promoting rhizobacterial phyla in the rhizosphere community, such as Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Acidobacteria. Mitigation of the stress responses is also exhibited due to the dynamic augmentation of genes such as czcA, arsH, copA, merC, nifHDK, norB, nosZ, nirSK, nrfA, napA, narG, and hzo.