Microbial diversity loss and plant genotype modulates rhizosphere microbial β-diversity to constrain soil functioning

β-diversity (community structure) of bacterial and fungal communities is a stronger predictor of ecosystem functions. Plant genotypes regulate the relationship between microbial diversity and ecosystem functions, with a significant link in different wheat genotypes. Biodiversity loss influenced the enrichment of keystone taxa (Burkholderia and Altemaria), which are related to specialized functions and crucial for network cohesion. Soil microbial alpha diversity is essential for driving ecosystem functions and processes. However, little is known about the beta-diversity affect community functions. Here, we combine distinct community inocula using the dilution-to-extinction approach with two wheat genotypes to study the effect of microbial diversity loss on rhizosphere community assembly processes, which are related to beta-diversity (between-habitat diversity), and the consequences for ecosystem functions within greenhouse experiment. Compared with alpha-diversity, the bacterial and fungal community beta-diversity are stronger predictors of ecosystem functions (organic matter degradation, phosphorus supply capacity and nitrogen supply capacity), plant genotypes regulated the relationship between microbial diversity and ecosystem functions, with ecosystem functions being significant link to microbial diversity under different wheat genotypes. Loss of microbial diversity decreased the abundance of Bacterial_ASV6 (Burkholderia) and increased Fungal_11 (Altemaria) within the restored rhizosphere soil. Null modeling analysis showed that the deterministic assembly processes are dominant in bacterial community and fungal high-diversity (alpha-diversity) community, associating with the change of specialized functions (organic matter degradation, phosphorus supply capacity and nitrogen supply capacity) that are correlated with microbial diversity and specific microbial taxa. In addition, these two species were key role for regulating to the network cohesion. Overall, our study pointed out that the regulation of community assembly by microbial diversity loss limits the development of soil ecological functions and weakens the stability of rhizosphere microbial network, highlighting the potential regulatory effect of microbial taxa distribution on microbial community stability and changes of specific ecological functions. (Figure presented.) © 2025 Elsevier B.V., All rights reserved.