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Let's get dirty! Plant roots are deeply embedded in clammy soil, and working with them means digging into the mud, hoping not to crush the fragile root branches and flimsy root hairs. In short, working with roots can be a tedious activity. This might partly explain why, over decades, roots could maintain a subsistence fairly hidden from the scrutinizing eyes of plant researchers—until the past few years. Plant breeding has been mainly driven by the search for aboveground traits; as a consequence, roots are now even claimed to be a potential key for a second green revolution (Gewin, 2010). Promising studies aiming to improve crop yields focus on root architecture and the genetics underlying root development. For instance, wheat lines exhibiting deeper and fast-growing roots were isolated and crossed with commercial cultivars, in the hope of generating drought-tolerant lines (Kirkegaard et al., 2007). Similarly, drought-stressed maize lines were shown to have a higher yield when specifically adapting their root structure by building an intercellular air space compared to maize varieties that were not able to adapt their root architecture (Zhu et al., 2010). As if handling abiotic stress would not be already a substantial task, roots are also garrisoned at the frontline against pathogens and pests. Soil-borne pathogens such as Fusarium, Pythium, or Phytophthora are infamous for being vicious parasites that can devastate entire harvests (Okubara and Paulitz, 2005). However, the lack of a convenient accessibility of root systems renders the task of controlling such pathogens more than challenging. Consequently, the knowledge about belowground defense responses is limited, in contrast to well-dissected aboveground mechanisms (Rasmann and Agrawal, 2008). Moreover, studies comparing root and shoot immune responses are scarce. In animal model systems, organ-specific antifungal immune responses are a well-known phenomenon (Lionakis et al., 2011). In plant-microbe models, pathological studies were historically mainly focused on either roots or shoots. Recent studies highlight an organ-specific immunity against fungal pathogens, pointing toward the fact that plants employ a “defense in depth,” a multi-layered organ-specific local and systemic defense system. Elucidating such a defense in depth for given pathosystems will be an important task for future studies in plant pathology.

More beneath the surface? Root versus shoot antifungal plant defenses