Differential regulation of cadmium accumulation by root microbiomes in high- and low-Cd accumulating rice cultivars

Cadmium (Cd) contamination threatens rice safety, and while low Cd-accumulating cultivars (LACs) offer a promising strategy, the mechanisms mediated by their root microbiome remain unclear. To address this gap, this study aimed to compare the rhizosphere and root endosphere bacterial communities of LACs and high Cd-accumulating cultivars (HACs) and to elucidate their roles in regulating Cd accumulation. A field experiment was conducted in Hengyang, China, to comparatively analyze the rhizosphere and root endosphere bacterial communities of LACs (CLiangYou755, ShenLiangYou5814, XiangWanXian-12) and HACs (MeiXiangZhan-2, YangDao-6, Changxianggu). Results confirmed that grain Cd content of LACs (0.14 ± 0.018 mg/kg) was significantly lower than that of HACs (0.23 ± 0.061 mg/kg). Critically, LACs rhizosphere exhibited significantly lower soil available Cd and higher pH compared to HACs, correlating with reduced Cd uptake. Physiological analysis indicated that LACs minimized Cd accumulation primarily by restricting root uptake and hindering root-to-shoot translocation. Microbiome profiling revealed that LACs assembled a potentially protective root microbial community. Specifically, their rhizosphere exhibited higher bacterial α-diversity and was enriched with taxa possessing potential Cd-immobilizing capabilities, such as Caldilinea and norank_f__norank_o__SJA-15, which were negatively correlated with soil available Cd and positively with pH. Within root endosphere, LACs specifically enriched key Cd translocation‑limiting taxa like Sideroxydans and specific operational taxonomic units (OTUs, e.g., OTU1619), collectively forming a microbial niche that further inhibits grains Cd accumulation. In contrast, HACs enriched taxa that may activate Cd, such as Bacillus and Geobacter in the rhizosphere, and were dominated by Anaerovorax in the root endosphere, exhibiting functional redundancy and assembly imbalance. In conclusion, this study elucidates that LACs mitigate grain Cd through a coordinated "rhizosphere co-shaping and root endosphere specific assembly" microbial strategy. These findings provide a crucial theoretical foundation for developing innovative, microbiome-based green technologies aimed at ensuring food security in contaminated regions.