Lessons from the Genomes: Rhizobacterial Ecology and Genomics

Abstract

The rhizosphere is a dynamic microbial hotspot where plant roots interact with diverse microorganisms, including plant-growth-promoting rhizobacteria (PGPR). Recent advances in genomic technologies, particularly genome sequencing, functional genomics, and metagenomics, have enhanced understanding of rhizobacterial ecology by revealing genetic traits associated with root colonisation, nutrient acquisition, and stress resilience under environmentally variable conditions. This review synthesises studies published over the past decade to examine the genetic basis of plant–microbe interactions. It evaluates the roles of horizontal gene transfer (HGT), niche adaptation, and the interplay between core and accessory genomes in structuring rhizobacterial communities. The review further highlights that gene presence does not consistently translate to in situ activity, reflecting context-dependent gene expression and environmental modulation of microbial functions. Key gaps include limited functional validation of candidate genes, constraints in linking genomic potential to ecological performance, and challenges associated with extrapolating laboratory-based findings to complex field environments. These insights inform ongoing efforts to develop genomics-guided microbial inoculants for sustainable agricultural systems.