Gene expression changes throughout the life cycle allow a bacterial plant pathogen to persist in diverse environmental habitats

Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between habitats is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate pathogen adaptation to water and soil, two environments that act as bacterial reservoirs, and compare this information with gene expression in planta. Gene expression in water resembled that observed during late xylem colonization, with an intriguing induction of the type 3 secretion system (T3SS). Alkaline pH and nutrient scarcity-conditions also encountered during late infection stages-were identified as the triggers for this T3SS induction. In the soil environment, R. solanacearum upregulated stress-responses and genes for the use of alternate carbon sources, such as phenylacetate catabolism and the glyoxylate cycle, and downregulated virulence-associated genes. We proved through gain- and loss-of-function experiments that genes associated with the oxidative stress response, such as the regulator OxyR and the catalase KatG, are key for bacterial survival in soil, as their deletion cause a decrease in culturability associated with a premature induction of the viable but non culturable state (VBNC). This work identifies essential factors necessary for R. solanacearum to complete its life cycle and is the first comprehensive gene expression analysis in all environments occupied by a bacterial plant pathogen, providing valuable insights into its biology and adaptation to unexplored habitats. Most bacterial pathogens have environmental populations outside their hosts that cause disease outbreaks. Very little is known about the genes necessary for adaptation and survival in these conditions because research on pathogenic bacteria has focused on their interaction with the eukaryotic host. In this work, we investigate global gene expression of the plant pathogen Ralstonia solanacearum in the two key environmental habitats that it occupies: water and soil. We describe extensive transcriptional reprogramming in response to each environment and unveil a number of candidate genes for adaptation to these harsh conditions. We discover that a costly virulence determinant (the type III secretion system) is transiently induced when bacteria are incubated in natural waters and identify pH as the main signal triggering this response. We propose that water conditions mimic those encountered in the plant xylem fluid and this enables the bacterium to be primed for infection. We also show for the first time that R. solanacearum induces in the soil the degradation of aromatic compounds and stress-response genes. We demonstrate that the oxidative stress response is essential for survival in this habitat.