Evolutionary and functional genomics reveal that Ralstonia wilt pathogens actively deploy antimicrobial warfare while leveraging physiological adaptations during plant infection

The xylem pathogens in the Ralstonia solanacearum species complex (RSSC) cause wilt diseases that threaten global food security. These diverse pathogens are highly adapted to the in planta environment where they proliferate and cause rapid, aggressive diseases. To understand the genetic underpinnings of these pathogens’ in planta fitness, we performed forward genetic screens in three RSSC species, using high-throughput random barcode transposon sequencing (RB-TnSeq). We quantified the competitive fitness of hundreds of thousands of mutants during stem colonization of susceptible tomato plants. We compared this in planta forward genetic screen with a prior forward genetic screen performed in a reductionist, plant-like environment: ex vivo xylem sap harvest from healthy tomato plants. The comparative genetic screens revealed both conserved and lineage-specific orthologs that enable RSSC’s pathogenic success. Consistently, these diverse pathogens navigated the opportunities and stressors in planta by maintaining a resilient cell envelope barrier, complementing the nutritional availability in xylem sap, fine-tuning their utilization of the host-manipulating type III secretion system, and dynamically regulating their gene expression through a suite of environment sensing and transcriptional regulatory proteins. Surprisingly, the strain-specific fitness factors shed light on ecological interactions beyond pathogen dominance of their susceptible host, even during the single-strain infections, the pathogens wielded arsenals of anti-microbial weapons. Specifically during growth in planta, each RSSC strain required a unique repertoire of type VI secretion system immunity proteins that provide self-protection to their own toxins. We contextualized the in planta fitness factors through evolutionary genomic comparisons of the RSSC wilt pathogens to their non-pathogenic neighbors. Together, these analyses reveal how conserved and lineage-specific fitness determinants have evolved to support pathogenic success in the plant vascular niche.