A TALE OF TWO BACILLI: COMPARATIVE GENOMIC APPROACHES FOR ASSESSING RHIZOSPHERE COMPETENCE STRATEGIES IN BIOCONTROL STRAINS

Rhizosphere competence, the capacity of microorganisms to colonize and survive in the highly-competitive plant root environment, is a prerequisite for the success of soil amended biocontrol agents (BCAs) and plant growth promoting rhizobacteria (PGPR). Previous studies have characterized a plethora of physiological traits that are associated with rhizosphere competence. We applied a comparative genomics-based approach to evaluate rhizosphere competence properties in two Bacillus spp. strains isolated from root surfaces of the medicinal tree Moringa oleifera. These strains showed differential in vitro antagonistic activity against the fungal phytopathogens Macrophomina phaseolina and Sclerotioum rolfsii. The genomes of the two organisms were sequenced, assembled and annotated using the SEED database; and subsequently screened against functional databases to identify genes encoding for secondary metabolites (antiSMASH), plant carbohydrate-metabolizing enzymes (CAZy) and antibiotic resistance (CARD). Collectively, based on the genomic comparisons and selected biochemical validation assays we determined that the two strains possess two different rhizosphere competence strategies: the first was characterized as a “Persistent colonizer”, with superior biofilm formation capacity, augmented virulence & antibiotic resistance, enhanced nutrient uptake (Fe, S, P, K), sporulation and denitrification capacity; while the second was coined a “Roamer/Scavenger”, with enhanced motility and chemotaxic capacity and more diverse metabolic potential. Given the above, we ascertain that root-associated bacteria can co-exist though spatial and metabolic niche differentiation by using different survival strategies and utilizing different organic compounds. Based on this realization, it seems highly logical that comprehensive biological control should focus on application of multiple BCAs with different ecological strategies that can work in tandem to alleviate biotic and abiotic hazards.