Cultivar-specific response of a root-associated microbiome assembly of rice to cadmium pollution

Rice (Oryza sativa L.) cadmium (Cd) contamination is a serious threat to global food security and human health. However, the response of rice root-associated microbiomes to Cd pollution remains unclear. This study investigate the interactions between the root-associated microbiome and plant metals using environmental and microbial analysis methods, to reveal the potential mechanisms of the root microbiomes regulating the Cd accumulation in rice. The results showed that the grain Cd concentrations of the two low-Cd accumulation (LA) cultivars were 34–46 % lower than that of the high-Cd accumulation (HA) cultivars, whereas the iron (Fe) content in the LA roots was significantly higher than that in the HA roots. The root Fe content was significantly negatively correlated with the Cd concentration of grain (R = −0.681, p < 0.05). 16S rRNA amplicon sequencing showed that rice planting significantly changed the diversity of the root-associated bacterial community and formed a unique core endophytic microbiome (such as Xanthobacteraceae and Sphingomonas) under Cd stress. LA cultivars assembled more root core microbial taxa, which promoted siderophore secretion and root Fe uptake, thereby inhibiting Cd uptake by rice. Chrome azurol S plate detection confirmed that the LA rhizosphere was enriched with 1–9-fold more siderophore-secreting microorganisms than the HA rhizosphere. This study provides new insights into the effects of root-associated microbiomes on Cd accumulation in plant and will help develop new strategies for the safe production of rice.