Plants are exposed to a fluctuating environment in which they need to respond to diverse changes of biotic and abiotic factors. For instance, roots that forage the soil for nutrients and water, are faced with water, mineral, and microorganismal distributions that fluctuate spatially and temporally in the soil. To function efficiently, roots therefore need to determine the biotic and abiotic properties of local soil environments and whether the optimal response in given environments is to sustain growth or instead to initialize defense programs. We are interested in how responses to abiotic and biotic factors are encoded in the genome, and how the thresholds at which responses are elicited are changed via natural genetic variation to allow for local adaptation. For this, we use the root of Arabidopsis thaliana, a plant species that has successfully colonized large parts of Eurasia; a range displaying stark variations of climates and soils. Using a systems genetics approach that integrates high throughput phenotyping, genome wide association mapping and functional genomic approaches, we identify genes and their variants that make roots respond differently to the same cues and study their relations to environmental variables. Among the most notable mechanisms that we found is a leucine-rich-repeat-receptor-kinase, which is involved in determining root growth responses to low iron levels, as well as to flagellin. Our data suggests a model in which iron availability and the presence of microbes are integrated by this and other receptor kinases.