An in-situ characterization of Triticum aestivum sheds light on the role of wheat genotype and agricultural practices on the below-ground microbiota

The below-ground microbiota plays a pivotal role in enhancing plant resilience to environmental stresses. Investigating microbial diversity within native agricultural systems is essential for understanding the potential of microbiota in sustaining crop health and productivity. Agricultural practices, including the selection of plant genotypes, are key determinants in shaping plant-microbe interactions. However, the role of plant genetic diversity in structuring below-ground microbiota has been only partially explored. Furthermore, many studies examining crop-microbiota interactions have been conducted under controlled conditions. In this study, we performed a two-year in situ survey of root and rhizosphere microbiota in 35 wheat ( Triticum aestivum ) genotypes grown in open fields under different organic agricultural practices, including unfertilized conditions, organic fertilization, and intercropping with faba bean. We characterized both bacterial and fungal communities and found that plant genotype, along with organic fertilization, were significant factors influencing the diversity and composition of root and rhizosphere microbiota. In addition, we showed that landraces varieties harbor a more diversified fungal microbiota when compared to modern varieties. Our study underscores the importance of incorporating wheat genetic diversity into agricultural strategies to enhance microbiota diversity.