To fully understand the plant and microbe interaction, it is crucial to reveal the changes in bacteria metabolism and gene expression during colonization. In my doctoral project, I will focus on understanding whether there is the reprogramming of the endophyte transcriptome and metabolism by colonization to the plant root. Further, it will be examined whether endophytes elicit specific or general responses for colonization in different lifestyles. The role of environmental factors in plant-microbe interaction is undeniable. For this reason, the effects of abiotic factors, especially nutrient deficiency, on the metabolism and transcriptome of free-living and endophytes will be examined. Thus, the changes that occur on the bacterial side of the plant-endophyte interaction will be understood.