Deinococcus sp. NH1 enhances cadmium tolerance in rice by modulating rhizosphere microbiome and plant metabolism

Cadmium stress threatens rice safety and farmland management. To investigate the role of high‑cadmium‑tolerant Deinococcus in alleviating plant cadmium stress, this study identified a strain, Deinococcus sp. NH1, with highly cadmium-tolerant and growth-promoting potential, via 16S rRNA gene sequencing and whole-genome average nucleotide identity analysis. Under cadmium stress conditions, inoculation with NH1 significantly alleviated growth inhibition in rice, resulting in notable increases in plant height, fresh weight, and root density. In soil containing 10 mg/kg cadmium, NH1 inoculation downregulated originally elevated genes related to cadmium detoxification and stress response, while upregulating biosynthesis and energy metabolism genes. Cadmium reduced rhizobacterial diversity, but NH1 restored diversity and induced community restructuring, significantly enriching beneficial microorganisms, such as Massilia and Haliangium. At the metabolic level, NH1 treatment altered the rhizosphere metabolome, in which terpenoids, and shikimates and phenylpropanoids such as 5-O-methylembelin and linoleate that showed significant positive correlations with the enriched microorganisms may play key roles. In summary, NH1 enhances rice tolerance to cadmium stress by regulating host gene expression, restoring and reshaping the rhizosphere microbial community structure, and driving beneficial microbe‑metabolite interactions. This study offers new insights into plant-microbe interactions in heavy metal stress mitigation.