Penicillium sp. inoculation alters rhizosphere microorganisms and root metabolism to reduce heavy metal accumulation in field rice

Microbiota-mediated bioremediation has emerged as a sustainable and eco-friendly strategy for mitigating heavy metal contamination in agricultural soils, yet the field-scale performance and mechanistic basis of functional microbial inoculants remain poorly understood. In this exploratory field study, we investigated the potential effects of a functional Penicillium sp. strain in heavy metal-contaminated paddy fields, focusing on its effects on the accumulation of chromium (Cr), cadmium (Cd), lead (Pb), and antimony (Sb) in rice ( Oryza sativa ), as well as the associated shifts in rhizosphere bacterial communities and root metabolic profiles. The results demonstrated that the concentrations of all four tested heavy metals were significantly reduced in the roots, shoots, and grains of rice plants under Penicillium sp. inoculation relative to the sterile medium control. Amplicon sequencing analysis revealed that fungal inoculation markedly decreased the relative abundance of Proteobacteria , while substantially enriching Acidobacteriota , Chloroflexi , and Methylomirabilota in the rhizosphere. Untargeted LC–MS metabolomic analysis further demonstrated that Penicillium sp. treatment drove prominent accumulation of key metabolites including sucrose, guanosine, and inosine, concurrent with significant depletion of malic acid and L-aspartic acid. Metabolic pathway enrichment analysis identified six core pathways that were substantially reprogrammed by fungal inoculation: glyoxylate and dicarboxylate metabolism, Calvin cycle-mediated carbon fixation, purine metabolism, glycine/serine/threonine metabolism, aminoacyl-tRNA biosynthesis, and starch and sucrose metabolism. Collectively, these findings establish an exploratory correlative framework linking Penicillium sp. inoculation to altered heavy metal accumulation in rice, reshaped rhizosphere bacterial communities, and reprogrammed root metabolic pathways.