Switch From Soil to Plant Host Lifestyle Is Mediated by rpoS Mutations in Bacterial Endophyte

Phenotypic switching in bacteria is a well-established evolutionary strategy that enhances fitness in response to changing environmental conditions. Here, we hypothesised that the observed phenotypic transition of the soil-dwelling Enterobacter sp. SA187—from yellow- to white-pigmented colonies upon plant root colonisation—reflects such an adaptive mechanism. This phenotypic switching is not host-specific but occurs consistently during the colonisation of various plant species. Through genome re-sequencing of switcher white colonies, we identified recurrent loss-of-function mutations in the rpoS gene compared to the yellow ancestral strain. Functional validation confirmed that mutations in rpoS are both necessary and sufficient to trigger the phenotypic switch, leading to widespread transcriptional changes affecting traits involved in plant colonisation, including motility, biofilm formation, metabolism, and growth rate. Metabolic profiling further revealed that the SA187 switcher variant exhibited enhanced fitness in conditions mimicking the acidic, sucrose-rich apoplastic environment of plant tissues, supporting the idea that this phenotypic switch represents a specific adaptation to the endophytic niche. Overall, our findings highlight the pivotal role of rpoS-mediated regulation in facilitating the transition of SA187 from a free-living to endophytic lifestyle and provide mechanistic insights into how bacterial symbionts dynamically adapt through phenotypic switching during host colonisation.