Molecular docking-assisted insights into nickel phytotoxicity and plant growth-promoting rhizobacteria-mediated stress alleviation in maize ( Zea mays L.) seedlings

Industrial and agricultural activities increase nickel (Ni) contamination in soils, threatening global food security. This study evaluated Ni-induced stress in maize (Zea mays L.) seedlings and the mitigating effects of two Ni-resistant plant growth-promoting rhizobacteria (PGPR). Maize seedlings were grown hydroponically and assigned to four treatments: control, 100 µM Ni, 100 µM Ni + Bacillus sp. strain Agri-17, and 100 µM Ni + Enterobacter ludwigii strain Agri-23. Growth, photosynthetic pigments, soluble proteins, antioxidant enzyme activities, and MDA content were evaluated. Potential Ni–protein interactions were additionally investigated using the MIB2 computational platform. Exposure to 100 µM Ni reduced root and shoot lengths by 35.8% and 29.8%, respectively, decreased soluble protein content by 14.1%, and markedly suppressed antioxidant enzyme activities, with CAT and APX decreasing by 58.6% and 55.9%, respectively. Compared with Ni alone, Ni + Agri-17 increased root and shoot lengths by approximately 3.3% and 5.5%, respectively, whereas Ni + Agri-23 did not improve either length parameter. However, Ni stress did not decrease dry-weight percentage and caused only minor changes in photosynthetic pigments. Under Ni stress, Ni + Agri-17 and Ni + Agri-23 increased soluble protein content by 17.2% and 16.8%, respectively, compared with Ni alone. The Ni + Agri-23 treatment increased chlorophyll a and carotenoid contents by 25.8% and 18.3%, respectively, while CAT activity increased by 59.3–67.7% relative to Ni alone. Compared with Ni treatment alone, APX activity reached approximately 3.4-fold in the Ni + Agri-17 group and 4.8-fold in the Ni + Agri-23 group. The SDS–PAGE analysis revealed qualitative treatment-dependent differences in protein banding patterns. The Ni treatment increased MDA content by 62.4% relative to the control, whereas PGPR inoculation did not significantly reduce MDA accumulation under Ni stress. Finally, molecular docking analysis provided computational predictions of potential Ni-binding interactions with maize proteins associated with growth, pigment biosynthesis, and antioxidant defense.