Endophyte Bacillus sp. RE35 Enhances Cd Trap in Rice Roots Via Root Cell Wall Remodelling During Colonisation

Cadmium (Cd) accumulation in rice poses a significant threat to food safety and human health. Plant growth-promoting endophytes (PGPEs) offer a promising strategy to mitigate Cd stress. Yet, the mechanisms underlying microbe-mediated reduction of Cd uptake, particularly through specific plant-microbe interactions, remain poorly understood. Here, we demonstrate that the root endophyte Bacillus sp. RE35, a Cd-tolerant and high-IAA producer isolated from rice, established an effective apoplastic niche and significantly enhanced Cd retention in roots through a multi-level mechanism. Successful colonisation of RE35 in the root apoplast, confirmed by the red fluorescent protein labelling, strain-specific gene quantification and colonisation-related genes analysis, promoted extensive root morphological remodelling via both de novo and salvage pathways of IAA biosynthesis under Cd stress. Notably, RE35 inoculation drastically reshaped Cd distribution, increasing cell wall-bound Cd by 64.7% while reducing shoot Cd accumulation by 24.1%-49.7%. This enhanced apoplastic trapping of Cd was attributed to a comprehensive cell wall remodelling program, activated through RE35-induced expression of plant receptor kinases (e.g., LRR-RLKs, LysM-RLKs) and the upregulation of key genes involved in the biosynthesis of pectin, hemicellulose and lignin. In parallel, RE35 modulated host Cd transport by downregulating influx transporter genes (OsNRAMP5, OsZIP5/9) and upregulating the vacuolar sequestration gene OsHMA3. Our findings reveal a Cd-responsive regulatory network where endophytes enhance apoplastic immobilisation by coordinating auxin signalling, receptor kinase activation and cell wall remodelling, providing a mechanistic basis for sustainable agriculture in contaminated environments.