Harnessing comparative genomics for trait specific synthetic plant symbionts - SYNBIONT

Objective

Climate change is undermining global food security through intensifying droughts, heat waves, and plant diseases. Microbial symbionts are increasingly recognized as key allies for climate-resilient agriculture, yet current approaches based on synthetic communities (SynComs) often fail under field conditions due to ecological instability. In parallel, comparative genomics has generated vast datasets linking host- and trait-associations for tens of thousands of bacterial genes, resources that remain largely untapped for rational symbiont design. The SYNBIONT project will harness these datasets to identify “trait cassettes”, gene clusters enriched in plant-associated bacteria and correlated with enhanced resilience to (a)biotic stresses. These cassettes will be integrated into Pseudomonas putida KT2440 (P. putida), followed by controlled Arabidopsis thaliana (A. thaliana) experiments under defined stress regimes. Validated resilience-associated genes will be combined into P. putida carrying 3-5 cassettes, engineered to cope with multiple simultaneous stresses, and benchmarked against traditional SynComs. Integrated phenotypic, transcriptional, metabolic, and physiological analyses will establish causal links between trait cassettes and plant resilience. This approach shifts the field from correlative observations to mechanism-driven, programmable symbionts. Key deliverables include: (i) a validated “PlantFit” atlas of trait-specific genes for stress resilience, (ii) a library of modular, ready-to-use cassettes for rapid deployment, and (iii) engineered P. putida chassis strains for mechanistic studies and translational agriculture. My expertise in synthetic biology and functional genomics, combined with the host lab’s strengths in comparative genomics and plant-microbe experimentation, provide the ideal foundation to execute this transformative, interdisciplinary project, as well as translate findings from A. thaliana into crops.