The rhizosphere microbiome, and especially bacteria, is essential for the plant’s life and health, forming different mutual beneficial relationships. Throughout evolution, bacteria have adapted to various habitats by adjusting their genomes in order to fit the changing environmental conditions, resulting in the development of additional functional traits. Epigenetic modifications in their DNA play a crucial role in their ability to thrive in such conditions. Climate change is a serious phenomenon, challenging the plant’s health and soil microbiome’s assembly, and bacteria must enhance their stability by using resistance, resilience, and redundancy, mainly by stress-driven epigenetic modifications. In this review, recent studies have been investigated in order to record the most abundant bacterial genera in the soil’s rhizosphere of 11 plants and at the same time to locate the role each one of them plays in plant’s health, which has also been regulated by epigenetic mechanisms, leading to the inheritance of diverse phenotypes. As a result, we propose that this field needs further investigation, and future research should be focused on testing the alterations of the abundance and possible epigenetic modifications on the DNA of the main bacterial genera in soil microbiome, from areas affected by the climate change consequences, in order to conclude to potential solutions for assisting the soil microbiome and plants to survive after such catastrophic conditions.