Provenance legacies override species effects in shaping oak rhizosphere microbiomes and metabolomes

As climate change drives more frequent and intense drought-heat extremes, selecting drought-tolerant trees is crucial for future forest resilience. However, the role of tree-microbial associations for this key trait remains largely unclear. In this study, we investigated how geographic origin, species identity, and intrinsic water-use efficiency (iWUE) shape the rhizosphere microbiome and root-rhizosphere metabolome of pedunculate (Quercus robur) and sessile (Q. petraea) oaks. In a six-year common garden experiment, we analyzed trees from both species, each grown from seeds from two distinct geographic origins, the upper Rhine basin (URB) and the north-east German lowlands (NGL), differing in water availability, using 16S and ITS rRNA gene based metabarcoding and untargeted metabolomics. We found a consistent legacy effect of seed origin on the composition of the prokaryotic rhizosphere microbiome and the metabolome, whereas tree species had no significant impact. The bacterial family Pseudonocardiaceae was enriched at trees from the drier origin NGL, while Blastocatellaceae and Micromonosporaceae were positively associated with iWUE across samples. Higher iWUE was furthermore significantly correlated with lower prokaryotic diversity and shifts in β-diversity, thereby linking a drought-adaptive host trait to the assembly of the belowground environment. Ellagic acid, a plant derived polyphenol associated with drought tolerance, was enriched in the drier origin NGL and linked to several prokaryotic taxa in correlation networks. The rhizosphere fungal community, however, was largely unaffected by origin or species. Solely fungal community evenness declined with increasing iWUE. Together, our findings suggest that ecotypic adaptation linked to origin can outweigh the effect of species-level traits in shaping the oak rhizosphere microbiome and metabolome. These findings emphasize that provenance-driven ecotypic adaptation can strongly influence plant–microbe interactions and underscore the need for provenance-aware selection and microbiome-informed assisted migration as strategies to strengthen forest drought resilience under global climate change.