Roots are the “hidden half” part of plants, which intriguingly take up a great part of plant life despite not being directly visible. Much research is going on about roots and despite much progress on understanding root anatomy and function, we are only just beginning to understand how these underground organs shape plant interaction with the biotic environment. Roots are developmentally flexible and integrate the (a)biotic environment into their shape. Overall, they are an excellent model system for scientific fields, ranging from genetics and cell biology to ecophysiology and ecology due to their stereotypic patterning, easy phenotyping, and applicability in microscopy-based imaging in growth setups. In recent years we have gained many insights into root form and function – including development and metabolic states – and we are now starting to put aspects of how plants utilize roots to communicate with the underground biotic environment into an empirical framework. Despite these intriguing aspects, roots are somewhat overlooked when it comes to agricultural qualities and might give rise to a wealth of knowledge applicable to increased crop yield and nutrient use efficiency. In this Methods Collection, we, therefore, aim to highlight broadly methods that utilize roots as a model.