NSF-BSF: Phenotypic heterogeneity as a driver of bet-hedging strategies in the plant microbiome

Plant-associated bacteria inhabit highly fluctuating environments, transitioning between soil, rhizosphere, and host tissues where selective pressures differ dramatically. Such ecological uncertainty favors bet-hedging, yet the mechanisms that generate phenotypic diversity in the plant microbiome remain poorly understood. This proposal integrates single-cell transcriptomics, genomic structural variation analysis, and engineered inversion reporters to uncover how transcriptional and genomic heterogeneity generate distinct bacterial subpopulations and shape plant colonization. We will define the regulatory programs underlying cell-state diversification (Aim 1), identify and track genomic inversions as heritable diversification mechanisms (Aim 2), and determine the ecological consequences of distinct genomic topologies across relevant plant-associated environments (Aim 3). Together, these studies establish a mechanistic foundation for understanding how microbiome members diversify strategies to thrive in fluctuating natural habitats.