RpoS mutations mediate Enterobacter endophytic life style switch from alkaline desert soil to acidic host apoplast

Enterobacter sp. SA187 is a facultative endophytic bacterium conferring multi-abiotic stress tolerance to various plant hosts. Upon interaction with plant tissues, a significant proportion of the typically yellow SA187 lose pigmentation. This phenotypic shift becomes more prominent with extended host plant colonization and under stress conditions, such as salinity. To explore the underlying mechanisms and ecological significance of this variation, we employed genome sequencing, comparative genomics, transcriptomics, and metabolic characterization. In all white SA187 variants, weidentified consistent point mutations in the rpoS gene, which encodes a global regulatory sigma factor. These rpoS loss-of-function mutations lead to alterations in gene regulation, affecting growth, morphology, biofilm formation, motility, oxidative stress responses and carotenoid production. Notably, the rpoS mutants demonstrated enhanced adaptability from a free living to an endophytic life style. Whereas the desert soil is characterized by highly alkaline conditions, the apoplast of the host plant is an acidic environment accompanied with the availability of distinct carbon sources. RpoS mutants allow life in the acidic and sucrose-rich apoplastic compartment, underscoring the role of genetic variation in bacterial adaptation to colonize plants. Overall design: To investigate the genetic changes occurring to SA187 upon plant colonization and defining the genetic and biochemical basis of the phenotypic variation observed.