Underground plant-associated microbiomes – soil, root, and rhizosphere – are critical to plant health and growth. Plant growth-promoting bacteria (PGPB) are being identified and tested to increase crop productivity and improve sustainability. However, the bacteria introduced as PGPB usually do not persist in soils, despite improving plant growth. If PGPB are promoting plant growth without establishing in the environment or plant microbiome, how are they continuing to influence plant growth? To answer this question, a recent study examined the influence of PGPB treatment on pokeweed. The PGPB inocula in this study had little influence on the rhizosphere microbiome assembly and did not colonize the plant roots. Instead, the PGPB induced DNA methylation in the roots. Methylation is an epigenetic mechanism that influences which genes are expressed and is sometimes passed on to offspring. Disrupting the inoculation-induced methylation patterns with a compound called Zeb greatly weakened the growth promotion, and the epigenetic changes remained functional after the inoculum was eliminated from the microbiome. While more research is needed, this study points to a new mechanism for PGPB-induced growth improvement.