New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions

Abstract

Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.

Keywords: PGPR – plant growth-promoting rhizobacteria; biotic and abiotic constraints; fungi; plant microbiome; sustainable agriculture.

FIGURE 1

The holistic overview of plant microbiome compositions, the interaction between plant and its associated microbes, function and its positive effect on plant growth and development under extreme conditions. Plant recruit and assembly beneficial microbes via exudation and constitute a healthy and beneficial microbial community. This microbiome improves plant health, alleviates abiotic stresses and provides a safeguard to the host exhibiting various direct and indirect mechanisms.

FIGURE 2

Plant microbiome engineering via biotechnological and conventional approaches. Host-mediated microbiome (indirectly selection of microbiome through utilization of host phenotype), artificial seed microbiome (artificial selection of microbiome and its integration/inoculation with seeds. This establish microbiome may evolve during the development and germination that consequently impact plant microbiome structure and function), Rhizosphere microbiome (bacterial competitiveness engineering) Synthetic microbiome (genetically engineered microbes inoculation to host plant) In situ microbiome (manipulation of native microbial community in their native context) Plant mycobiome (optimization and improvement of beneficial plant–fungal interactions).

FIGURE 3

Plant Microbiome provides key functions for plant health and its protection. Plant microbiome offers vital services for plant health. It facilitates biogeochemical cycling of plant nutrients, assist plant growth under biotic and abiotic conditions, induces systemic acquired resistance (SAR) and induces systemic resistance (ISR) in plant against plant pathogen. Inversely, Plant microbiome synchronously encounters biotic and abiotic stresses which are the substantial drivers that influence or alter microbiome diversity and functionality.