Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production

Abstract

Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.

Keywords: Agriculture; Microbiome; Plant–microbe Interactions; Rhizosphere; Signaling.

Graphical abstract

Fig. 1

Schematic flow of development of strategies for analyzing plant microbiome from different compartments and use of Omics approach for understanding of cultivable and uncultivable microbiome for plant growth promotion.

Fig. 2

Engineering rhizosphere microbiome of susceptible plant by manipulating healthy microbiome from resistant plant.

Fig. 3

Flow chart showing Metagenomic data analysis workflow.