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

Background and Aims : Understanding how tillage and fertilization influence soil microbes and crop quality is crucial for sustainable agriculture. This study examined how variations in tillage intensity and fertilization shape soil microbial communities and, through these shifts, affect the nutritional quality of maize and wheat. This approach revealed clear links between microbial community composition and crop nutrient outcomes. 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 high input) across fifteen nutrient treatments. Sixty-four soil and grain samples were analyzed. Soil microbial diversity and functional potential were assessed through metagenomic sequencing, while grain content was determined using standardized biochemical assays. Results : Within long-term trial contexts, it was demonstrated that tillage–fertilization combinations modulate soil microbiomes in ways that propagate to grain nutritional quality. Ploughing increased alpha diversity (p < 0.05) but favored generalist, stress-tolerant taxa associated with rapid nutrient turnover, aligning with higher carotenoid and lipophilic antioxidant contents. In contrast, deep loosening supported more crop-specific, functionally specialized, and apparently more stable microbiomes, reflected in greater accumulation of water-soluble antioxidants. Balanced fertilization was associated with denser, better-connected microbial networks, while excessive inputs disrupted ecological equilibrium and weakened the translation of soil functions to nutritional traits. Conclusions : Crop nutritional quality can be tuned via the soil microbiome: under moderated inputs, ploughing tends to raise carotenoids/lipophilic antioxidants, whereas deep loosening with balanced fertilization favors water-soluble antioxidants; excessive fertilization disrupts microbial balance and weakens these benefits.