Consistent Microbial Assembly in the Rhizosphere of Crop Wild Progenitors

ABSTRACT Aim Microbiome rewilding seeks to harness plant‐microbe interactions for sustainable agriculture, assuming that ancestral microbial partners have been lost during domestication and geographical spread. Designing microbiome rewilding strategies requires a quantitative and predictive understanding of the fundamental ecological processes—selection, dispersal, and drift—driving microbial assembly and persistence in the rhizosphere of crop wild progenitors (CWPs). Location Global. Time Period Present. Major Taxa Studied Rhizosphere bacteria and fungi. Methods Here, we leveraged a global survey of the CWPs of 10 major crops across their native habitats to assess the roles of selection, dispersal, and drift in shaping rhizosphere microbial communities. We combined compositional and phylogenetic turnover metrics with local network analyses to evaluate community assembly and structure in response to environmental gradients. Results We found host‐driven selection, reflected by low phylogenetic turnover at the whole‐tree level, but also selection driven by differences among individual plants, as indicated by high turnover among closely related taxa. The high level of compositional turnover found suggests dispersal limitations, which in the context of CWPs, may indicate host‐mediated filtering of external microbial taxa. The network structure was constant across CWPs; however, bacterial and fungal structures diverged, pointing to distinct community organisations. Bacterial communities presented higher modularity and lower clustering than fungal communities. Climate, especially seasonal temperature and precipitation, was the main driver of both bacterial and fungal structures. However, host identity best predicted bacterial structure, while NDVI, a proxy for vegetation status, better explained fungal patterns. Main Conclusions Bacterial and fungal communities are shaped by consistent assembly processes across CWPs, but their structures diverge. With the identification of the assembly processes driving microbiome composition in the rhizosphere of CWPs, this work paves the road to incorporate microbiome rewilding in the toolbox of sustainable agriculture.