Multi-omics approach of wheat varieties, agronomic practices and functional microbiome for sustainable precision agriculture

The soil and rhizosphere microbiome are essential for plant health and agroecosystem sustainability, regulating nutrient cycling, stress resistance, and crop yeld. In wheat, microbial composition and function are strongly influenced by both varietal genetics and agronomic practices, including fertilization and crop protection measures. This study assessed how geography, agronomic practices, and wheat cultivars (Triticum durum and T. aestivum) influence soil microbial communities. Soil samples collected from eleven modern varieties grown across northern, central, and southern Italy were analysed using a multi-omics approach, combining metagenomics, metabolic pathways, and detailed agronomic data on fertilization and pesticide use. Microbial functional diversity was evaluated using Biolog EcoPlates™, with AWCD as an indicator of metabolic activity, the microbial communities were characterized by means of targeted 16S rRNA gene sequencing (using Oxford Nanopore) and the potential functions of the microbial communities were predicted using PICRUSt2. Soil microbial communities associated to T. aestivum showed significantly higher metabolic activity than those of T. durum (p < 0.01). Multivariate analyses revealed that wheat variety and agronomic practices jointly influenced microbial diversity, metabolic capacity, and predicted functions, with T. durum favouring Bacilli-dominated communities and T. aestivum supporting a more diverse microbiota. Moreover, gene analysis findings showed that genotype and agronomic management act synergistically in shaping distinct microbial communities with specific metabolic and functional profiles, including carbon sequestration activity, organic matter degradation and phosphate solubilization. This study provides new insights and perspectives for the validation of sustainable and personalized agronomic strategies, integrating variety selection with microbiome management to enhance crop resilience and productivity. These findings underscore the importance of microbiome-aware crop management not only for improving plant performance, but also for preserving soil ecological integrity, thereby contributing to broader One Health objectives that connect environmental sustainability, agricultural practices, and human nutrition and well-being. Acknowledgements: METROFOOD-IT project has received funding from the European Union - NextGenerationEU, PNRR - Mission 4 “Education and Research” Component 2: from research to business, Investment 3.1: Fund for the realisation of an integrated system of research and innovation infrastructures - IR0000033 (D.M. Prot. n.120 del 21/06/2022)