PhD defence: Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops

Plant domestication has transformed wild species into high-yielding crops but simultaneously has reduced both genetic and microbial diversity. Using potato (Solanum tuberosum) as a model, this work explores how domestication and agricultural intensification reshaped plant-microbiome interactions and how restoring ancestral microbes can recover lost functions.

We showed that in the Andes, the center of origin of the potato, habitat domestication homogenized soil chemistry and microbial composition, erasing natural ecological gradients. Native soils supported distinct microbial assemblages, and their depletion in agricultural soils corresponded with reduced disease suppression. Reintroduction of native taxa through a fourteen-member synthetic community restored resistance to potato late blight (Phytophthora infestans), demonstrating the functional basis of microbiome rewilding.

Likewise, diploid hybrid breeding experiments revealed that heterosis expression in true potato seed systems was microbially mediated: hybrids maintained immune balance and stable microbiomes, whereas inbreds exhibited stress and immune overactivation.

Altogether, this research established that the microbiome is a central component of domestication that could be restored. Rewilding crops with ancestral microbial partners represents a rational strategy to enhance productivity and resilience in sustainable agriculture.