Multi-omics approaches for deciphering the microbial modulation of plants' genetic potentials: What's known and what's next?

Plant–microbe interactions leading to altered expression of plants' genetic potentials are the subject of an increasing number of studies. In recent years, there has been a growing body of research reporting on the phenomenon of differentially-expressed genes (DEGs) in plants that have been inoculated with certain strains of symbiotic microbes, either bacterial and fungal. Microbial treatments are already being used to increase crop yields in several parts of the world, with commercial versions being marketed. While abundant evidence is confirming the impacts of endophytic microbes on plants' gene expression, the molecular events that occur within the plant's cellular environment are not established, and investigations on these aspects of plant-microbial interaction are still limited. This article reviews current understanding of the several biochemical and molecular mechanisms whereby plants' genetic potentials can be elicited or influenced by beneficial microbes. Means for further research and progress for applying this knowledge for crop improvement are discussed. •Microbes living within plants can alter host plants' gene expression significantly.•The modulation of plants' genetic potential by microorganisms involves complex regulatory networks based on signal exchanges between host plants and microbial symbionts.•High-throughput ‘omics’ platforms now coming into wider use can illuminate the complexity and the effects of plant-microbial symbiosis.•Improved understanding on the mechanisms involved in plant-microbe interactions could contribute to more productive and sustainable agriculture.