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Summary Most plant–microbe interactions are facultative, with microbes experiencing temporally and spatially variable selection. How this variation affects microbial evolution is poorly understood. Given its tractability and ecological and agricultural importance, the legume–rhizobia nitrogen‐fixing symbiosis is a powerful model for identifying traits and genes underlying bacterial fitness. New technologies allow high‐throughput measurement of the relative fitness of bacterial mutants, strains and species in mixed inocula in the host, rhizosphere and soil environments. I consider how host genetic variation (G × G), other environmental factors (G × E), and host life‐cycle variation may contribute to the maintenance of genetic variation and adaptive trajectories of rhizobia – and, potentially, other facultative symbionts. Lastly, I place these findings in the context of developing beneficial inoculants in a changing climate.