Plant Microbiome Engineering for Sustainable Agriculture

With a rising human population and the impact of climate change, sustainable agriculture is crucial for meeting societal needs. Traditional methods of enhancing crop productivity through chemical fertilizers and pesticides have led to environmental degradation. Therefore, we must adopt sustainable solutions that decrease our dependence on agrochemicals while boosting farmland productivity. One sustainable approach to enhance plant growth is by using plant growth-promoting rhizobacteria (PGPR), which can improve nutrient use efficiency, provide immunity and growth-stimulating hormones. Current agricultural practices have disrupted and neglected this important microbial community, resulting in a decreased rhizobacteria diversity and dysbiosis of beneficial crop microbiomes. Moreover, the complexity of the preexisting soil microbial community and the variability of soil abiotic conditions create challenges for supplementing desirable soil bacteria into agricultural fields. This complex interaction network between the plant host, environment, and soil microorganisms hinders the development of designer agricultural microbiomes with robust plant benefits. Hence, a fundamental understanding of the plant-microbiome communication is essential to re-optimize this relationship.

Plant genotype plays a critical role in biasing the composition of the microbiome, primarily through the secretion of carbon-rich exudates. By altering the exudate composition through plant genetic engineering, we can strategically manipulate and target the microbiome, fostering successful colonization by specific microbes. For this, we developed a workflow identifying plant metabolites in root exudates controlling the colonization and enrichment of various specific PGPR. The final aim is to engineer plant root exudates to enrich functional PGPR solubilizing nitrogen and phosphate under nutrient stress for sustainable plant growth.