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Background  Conventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use  13 CO 2  stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon.    Results  Metabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were  Streptomycetaceae  and  Burkholderiaceae . Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the  Burkholderiaceae  family, among other core enriched taxa such as  Pseudomonadaceae,  were able to use root exudates, but  Streptomycetaceae  were not.    Conclusions  The consistent enrichment of  Streptomycetaceae  and  Burkholderiaceae  within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While  Streptomycetaceae  did not utilise root exudates in the rhizosphere, we provide evidence that  Pseudomonadaceae  and  Burkholderiaceae  family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.    Supplementary Information  The online version contains supplementary material available at 10.1186/s40793-021-00381-2.

Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome