Beneficial bacteria and arbuscular mycorrhizal fungi mitigate Cd+Zn stress in tomato through coordinated changes in ion homeostasis, root exudation and rhizosphere microbiome structure

Heavy metal (HM) pollution from agricultural practices accumulates in soils, moving through crops and food chains, posing significant environmental concerns that threaten ecosystem integrity and human health. In this study, the morphophysiological traits e.g., biomass, relative water content, membrane stability, PSII efficiency and oxidative stress markers, as well as the allocation of metals and nutrients in different plant tissues, and the changes in the root microbiota are assessed in tomato plants exposed to combined Cd+Zn stress and inoculated with two microbial biostimulants (MB): a plant growth-promoting rhizobacterium (PGPR) and an arbuscular mycorrhiza (AMF) consortium. Cd+Zn exposure affected morphophysiological traits, reducing shoot and root biomass (12% and 9.5%, respectively) and membrane stability by 37.7% in tomatoes, and reshaped root exudation patterns, but MBs improved tomato resilience by mitigating these effects. AMF improved root development and metabolite accumulation with antioxidant, membrane‑protective, and metal‑chelating functions. PGPR effectively restored shoot fresh and dry biomass, reduced leaf ROS accumulation, and limited Cd accumulation across tomato organs. Specifically, it induced more complex metabolic reprogramming, reducing lipid and phenolic turnover while accumulating steroidal saponins and N‑containing compounds. At the rhizosphere level, PGPR significantly increased bacterial and fungal richness relative to the control (Chao1, p ' 0.01 and p ' 0.05, respectively). Multi-omics integration further showed strong metabolite–microbiome associations (r ' |0.9|), with PGPR treatment enriching fungal families (e.g., Aspergillaceae and Chaetomiaceae) and bacterial orders (e.g., Flavobacteriales and Rhizobiales), which were positively correlated with root exudates and potentially involved in organic matter turnover, nutrient cycling, and HM detoxification.