Variations in microbial assemblage between rhizosphere and root endosphere microbiomes contribute to host plant growth under cadmium stress.

Microbial assemblages in the rhizosphere and root endosphere compartments exhibit variations in response to environmental stressors. However, whether these variations contribute to plant growth under abiotic stress remains unclear. In this study, we conducted a comparative study to characterize the assembly of the rhizosphere and root endosphere microbiome between two ecotypes of Sedum alfredii , a perennial herb plant across Asia, under cadmium (Cd) stress. Our results revealed that under Cd stress, the fresh weight of the Cd-accumulating ecotype (AE) was significantly higher than the non-accumulating ecotype (NAE). The evenness and diversity of the rhizosphere microbiome were significantly reduced, but the complexity was significantly increased in AE compared to NAE. Crucially, we found that the changes in microbial dissimilarity were correlated with plant performance under Cd stress. Moreover, we identified that microbial network complexity has a greater number of positive associations with the rhizosphere keystone operational taxonomic units (OTUs) identified from the AE than from the NAE. Our results also demonstrated that phenolic compounds, including benzenoids and flavonoids, play a crucial role in shaping the distribution of keystone OTUs in both AEs and NAEs by functioning as carbon sources and semiochemicals. In summary, our study provides new insights into how changes in microbial assemblage between rhizosphere and root endosphere microbiomes contribute to plant growth under abiotic stress. IMPORTANCE In this study, we revealed that the variation in rhizosphere and root endosphere microbial assemblage between host plant ecotypes contribute to their differential abilities to withstand cadmium (Cd) stressors. Furthermore, our study found that phenolic compounds, such as benzenoids and flavonoids, could function as both essential carbon sources and semiochemicals, thereby contributing to the assemblage of rhizosphere microbiome to resist Cd stress. Our findings provide new insights into the mechanisms that drive the differential assemblage of rhizosphere and root endosphere microbiomes to enhance plant growth under abiotic stress.