To understand the growth-promoting and
disease-inhibiting activities of
plant growth-promoting
rhizobacteria (PGPR) strains, the genomes of 12
Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that
gene family similarity among Bacillus genomes ranges from 32-90%, with 2,839 genes within the core
genome of B. amyloliquefaciens subsp. plantarum (now B. velezensis). Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and
colonization of roots and / or leaves, including 73 genes uniquely associated with subsp. plantarum (now B. velezensis) strains that have predicted functions related to signaling, transportation,
secondary metabolite production, and
carbon source utilization. Although B. amyloliquefaciens (now B. velezensis) strains contain
gene clusters that
encode many different secondary metabolites, only
polyketide biosynthetic clusters that
encode difficidin and macrolactin are conserved within this
subspecies. To evaluate their role in
plant pathogen biocontrol, genes involved in
secondary metabolite biosynthesis were deleted in B. amyloliquefaciens (now B. velezensis) strain, revealing that difficidin expression is critical in reducing the severity of
disease, caused by
Xanthomonas axonopodis pv. vesicatoria in tomato plants. This Example defines genomic features of PGPR strains and links them with biocontrol activity and with host
colonization.