Soil management–dependent shifts in microbial diversity and nutrient − related functions ultimately shape the nutritional composition of maize and wheat

Abstract Background and aims Tillage and fertilization are key soil management practices that influence soil microbial communities, nutrient cycling, and crop performance. However, how management − induced microbial changes relate to crop nutritional performance remains insufficiently understood. Therefore, this study aimed to evaluate the effects of ploughing and deep loosening, as well as contrasting fertilization regimes, on soil microbial community composition and diversity, and to relate these practices and microbial responses to grain nutritional traits, including protein content, antioxidant activity, and carotenoid concentration in maize and wheat. Methods Field experiments were conducted within established long − term trial sites, using two tillage methods, ploughing and deep loosening combined with two fertilization regimes (moderate and extensive input) across fifteen nutrient treatments. Sixty − four soil and grain samples were analyzed. Microbial diversity and functions were analyzed by metagenomics, and grain traits by biochemical assays. Results Tillage and fertilization significantly altered soil microbial communities and their network organization. Ploughing increased alpha diversity ( p < 0.05) but favored generalist, stress − tolerant taxa, whereas deep loosening supported more specialized assemblages. Balanced fertilization enhanced network density and modularity (density up to 0.46; modularity 0.108–0.121), while extensive fertilization disrupted network structure. These microbial shifts were mirrored in grain traits. Ploughing increased carotenoid concentrations ( p < 0.001), lipophilic antioxidants showed no treatment differences ( p > 0.05), and deep loosening was linked to greater accumulation of hydrophilic antioxidants ( p > 0.05). Conclusions Soil management shapes crop nutrition: ploughing boosts carotenoids, deep loosening favors hydrophilic antioxidants, while excessive fertilization disrupts these benefits.