Paraburkholderia phytofirmans PsJN colonization of rice endosphere triggers an atypical transcriptomic response compared to rice native Burkholderia s.l. endophytes

Plant microbiome recently emerged as a reservoir to develop sustainable alternatives to chemical fertilizers and pesticides. However, the response of plants to beneficial microbes appears as a critical issue to understand the molecular bases of the interaction of plants with their microbiota. In this study, we combined root colonization, phenotypic and transcriptomic analyses to decipher the commonalities and specificities of the response of rice to closely related Burkholderia s.l. endophytes. In general, these findings suggest that a rice non-native Burkholderia s.l. strain, Paraburkholderia phytofirmans PsJN, is able to colonize the root endosphere while triggering a markedly dissimilar response compared to rice-native Burkholderia s.l. strains. This shows the variability of the response of plants to microbes from different hosts of origin. The most staggering finding from the investigation was that a much more conserved response to the three endophytes used in this study is triggered in leaves compared to roots. Additionally, the transcriptional regulations of genes related to secondary metabolism, immunity and phytohormones appears as markers of the strain-specific responses. Future studies must investigate if these findings can be extrapolated to other models of plants and beneficial microbes to further advance the potential of microbiome-based solutions for crop production.