The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization.

Plant-beneficial microbes have great potential to improve sustainability in agriculture. Still, managing beneficial microbes is challenging because the impact of microbial dormancy on community assembly across the soil, rhizosphere, and endosphere is poorly understood. We address this gap with the first documented use of Biorthogonal Non-Canonical Amino Acid Tagging (BONCAT) to probe active microbes in the soil-to-root gradient. Using nodule-forming legume IMPORTANCE: Most soil microbes are dormant, so they must exit dormancy to have the potential to carry out plant-beneficial functions. It is unclear if dormant microbes revive in proximity to plant-produced resources and if overcoming dormancy in the soil is important for successful plant colonization. We use a novel microbial activity probing technique for the first time on and in plant roots, and with it, we observe microbes increased in activity 10× inside plant tissues compared to the soil, likely in response to plant-produced resources. In complex, native microbial communities, we observe that microbes that are active and abundant are more likely to colonize plant roots successfully than just abundant microbes. Our research shows that plants could be leveraged to promote a distinct active microbial community from the native soil, a discovery that has the potential to improve sustainability in agriculture.