In natural and agricultural environments, plants are commonly exposed to antibiotics, which accumulate in soils due to natural production by microorganisms or to anthropogenic activities. In this issue, Gudiño et al. (on pp. 2086–2098) report on the effects of β-lactam antibiotics on root development, which are associated with changes in auxin accumulation and the production of Reactive Oxygen Species and other compounds involved in defense against fungal pathogens. This study therefore warns of the interference of antibiotics upon potentially beneficial interactions with known endophytes.