Deciphering plant-microbiome communication for sustainable crop production

Discovering and application of plant growth-promoting rhizobacteria (PGPR) as biofertilizer and biocontrol agents is on the cutting-edge of sustainable crop production. For long, studies on PGPR were focusing on discovering rhizobacteria possessing specific metabolic functions, majorly biosynthetic function, such as the production of antibiotics. Meanwhile, computational tools, such as antiSMASH, that predict biosynthetic gene clusters (BGCs) from bacterial genomes have been developed to predict these functions. Opposite to synthetic metabolism, how catabolic capability could affect the function of rhizobacteria was less studied. Because plants secret a complex matrix of root exudates, making the rhizosphere a nutrient-rich niche to compete for, the ability to utilize metabolites in the root exudates is important for bacteria to colonize the rhizosphere. However, we neither have much knowledge nor a computational tool to study about the catabolic function of beneficial rhizobacteria. In this study, we propose that catabolic gene clusters in bacterial genome indicate the potential to utilize root exudates. We aim to extend the function of AntiSMASH to predict catabolic gene clusters in rhizobacteria and use them to predict rhizosphere colonization and link them to disease suppression.