Soybean domestication alters rhizosphere microbial assembly and disrupts the potential bacteria-protist relationships.

Crop domestication has long been known to reshape rhizosphere microbial communities, yet research has focused disproprotionately on bacteria and fungal responses to crop domestication while neglecting protist communities. Protists, as key microbial predators regulating bacterial populations and thereby their functionalities, remain understudied in this context. Here, we investigate the influence of soybean domestication on both bacterial and protist communities, with a focus on the reorganization of ecological strategies, specifically generalists and specialists, within these microbiomes. We analyzed 270 rhizosphere samples from 27 domesticated and 63 wild soybean varieties. Domestication significantly altered community compositions of bacterial communities, with wild soybeans harboring higher proprotions of Pseudomonadota (71.4 %) and Bacillota (4.8 %), while domesticated soybeans exhibited an enrichment of Bacteroidota (11.0 %). Protist communities also diverged: wild soybeans were dominated by Cercozoa (58.2 %) and Gyrista (23.5 %), while domesticated plants had more Ciliophora (7.1 %) and Evosea (5.7 %). Domesticated soybeans hosted fewer generalist and specialist bacteria but more generalist protists, suggesting divergent microbial responses to domestication. Correlation analyses revealed that bacterial and protist generalists exhibited strong positive correlations with each other. At the same time, bacterial and protist specialists also showed positive correlations in wild soybeans-patterns that were largely absent in their domesticated counterparts. Functionally, wild soybeans supported more ureolytic and methylotrophic bacteria, while domesticated soybeans favored nitrate-respiration taxa. Notably, predatory protists in wild soybeans were significantly correlated with bacteria involved in carbon and nitrogen cycling, a key ecological relationship lost with domestication. These findings suggest that domestication exerts different selection pressures on bacteria and protists, disrupting potential relationships between bacterial and protist functional groups.