Plant-associated microbial communities are well known to affect fitness and performance of their hosts. Within the BMBF-funded project RhizoTraits, we investigate how the rhizosphere microbiome of crop plants contributes to their tolerance to drought stress. Our hypothesis is that plant traits fostering the formation of microbial communities which promote resilience to drought have been compromised in the breeding of modern, yield-optimized varieties. Focusing on maize as a model crop, we are currently performing a systematic comparison between a selection of modern varieties and old landraces. In a large-scale greenhouse experiment, we have recorded the performance of 48 varieties under drought stress. Based on their water use efficiency, we selected 12 varieties for an in-depth analysis in the field. Here, we give an insight into the currently ongoing analysis of the microbial community in the samples from the greenhouse and field experiments. Our methods include the assessment of microbial abundances and activities using basic indicators such as root-associated extracellular enzyme activities. Rhizosphere bacterial and microeukaryote community composition is investigated via SSU rRNA amplicon sequencing. By linking our findings with data on root architecture, rhizodeposition and edaphic properties, we aim to contribute to the development of a holistic understanding of the mechanisms and functions within the plant-microbe system under water limitation. This will provide a valuable basis for considering plant-microbe interactions in the development of future crop varieties and agricultural practices.