Distinct impacts of soybean domestication on rhizosphere bacteria and protist assembly

Domestication crop reshapes rhizosphere microbial communities through long-term artificial selection. However, current research has predominantly focused on environmental filtering effects on microbial community composition, overlooking niche-specific taxonomic characteristics of microbial species. Critically, generalist and specialist taxa play divergent ecological roles: generalists drive functional redundancy to buffer environmental fluctuations, whereas specialists mediate niche-specific processes such as pathogen suppression or nutrient acquisition. This study integrates niche differentiation theory and multi-trophic interaction analysis to systematically dissect shifts in bacterial and protist generalists/specialists across 27 domesticated and 63 wild soybean accessions (comprising 270 rhizosphere samples), unraveling how artificial selection reconfigures microbial niche partitioning and functional complementarity. The results showed that the rhizosphere microbiota of soybean was significantly reorganized during the domestication process, and the rhizosphere bacteria of wild accessions were significantly enriched in Pseudomonadota (71.40%) and Bacillota (4.81%), and the rhizosphere bacteria of domesticated accessions were significantly enriched in Bacteroidota (11.02%). In terms of protist, the wild species were significantly enriched in Cercozoa (58.22%) and Gyrista (23.48%), while the domesticated species were enriched in Ciliophora (7.06%) and Evosea (5.74%). Domesticated soybeans exhibited reduced diversity in both generalist and specialist bacterial taxa, whereas protist generalists showed increased diversity. Correlation analysis revealed significant correlations between the relative abundances of specialist/generalist microbial taxa in the rhizosphere of wild soybeans, whereas no significant correlations were observed in domesticated soybeans. The wild soybean rhizosphere was enriched with bacterial taxa associated with ureolysis and methylotrophy, while the domesticated soybean rhizosphere was enriched with taxa linked to nitrate respiration. Functional analysis further indicated a significant positive correlation between the relative abundance of predatory protists and bacteria involved in carbon and nitrogen cycling in the wild soybean rhizosphere, but this relationship was not significant in domesticated soybeans. Our results provide a theoretical basis for uncovering domestication-driven microecological evolution and advancing sustainable agroecosystem practices.