Genome scale cis acting element cres editing confers Bacillus pumilus LG3145 plant beneficial functions

Crop growth depends on beneficial functions performed by rhizosphere microorganisms such as Bacillus spp. However, long-term synthetic fertilizer application to soil always degrades these functions. We developed a modified CRISPR-Cas9 system using non specific single-guide RNAs to disrupt the genome-wide cis-acting elements of carbon catabolite repression in a wild-type Bacillus pumilus, which conferred its dual-plant-benefit properties. Most of the mutations occurred around the imperfectly matched cis-acting elements (cre-like sites) in genes that were mainly involved in carbon and secondary metabolism pathways. The comparative metabonomics and transcriptome results revealed that carbon is likely transferred to some pigments, such as riboflavin, carotenoid, and lycopene, or non-ribosomal peptides, such as siderophore, surfactin, myxochelin, and bacilysin, through the pentose phosphate and amino acid metabolism pathways. These findings collectively suggested that the mutation of global cre-like sequences in the genome perhaps alters carbon flow, thereby allowing beneficial biological interactions between the rhizobacteria and plants.