Abstract
Rising population, climate change, and human activities intensify abiotic stress in plants. Conventional methods, such as chemical use and breeding, pose ecological risks. This study explores sustainable bioremediation using fungi and bacteria to enhance tomato plant resilience against arsenic and crude oil stress. Results showed that microbial inoculation significantly improved plant growth by enhancing stress tolerance and physiological functions such as water content and photosynthesis. Additionally, it reduced oxidative stress markers, indicating improved plant health. The roots of stressed seedlings showed significant anatomical differences compared to the control group, with stress-induced tissue damage and deformation of root epidermal cells affecting nutrient and water absorption. Additionally, our analysis of gene expression under arsenic and crude oil stress, with and without the introduction of microbial strains MGRF2, SL1, and SPSB2, revealed that microbial inoculation generally downregulated the expression of the examined genes under normal conditions. Different microbial strains respond uniquely to arsenic and crude oil stress by altering gene expression. Specifically, they upregulate genes associated with signaling pathways such as JA, heavy metal tolerance, and DREB, potentially reducing toxicity. Microbial strains MGRF2, SL1, and SPSB2 offer eco-friendly solutions by easing stress and enhancing plant growth for sustainable agriculture. GRAPHICAL ABSTRACT: The diagram illustrates the impact of microbial inoculation and arsenic treatment on plant growth and defense mechanisms under crude oil-contaminated soil conditions. Initially, soil is treated with crude oil and inoculated with beneficial microbial strains (MGRF2, SL1, and SPSB2). These microbes colonize the plant roots, triggering a cascade of plant-microbe interactions. This leads to changes in plant morphology, physiology, and gene expression. Subsequently, arsenic (As) treatment is applied, influencing both primary and secondary metabolite production. The microbial presence enhances nutrient uptake, promotes plant growth, and strengthens plant defense responses, ultimately mitigating the adverse effects of crude oil and arsenic stress. [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08294-3.