Taxonomic and functional diversity of bacteria and fungi in the rye root environment is affected by landrace genotype

The plant microbiome is essential for plant life, with root compartments hosting diverse bacterial and fungal communities that support plant survival and productivity. This study investigates whether rye ( Secale cereale L.) landraces, which may reflect local adaptations, harbor distinct root-associated microbiomes compared to modern varieties. Using metabarcoding (bacterial 16S rRNA and fungal ITS2), we characterized microbial communities in the rhizosphere and root endosphere of three local landraces and two modern varieties cultivated in two sites of the Italian Western Alps. Root compartment and growing site emerged as the main factors shaping microbial community structure, but genotype-specific differences were also observed in endospheric communities. Local landraces formed distinct microbial clusters compared to modern varieties, with differential abundances of key taxa such as Bradyrhizobium and Mortierella . Functional predictions further indicated significant variation in several bacterial metabolic pathways, suggesting that host genotype affects microbial adaptation. These findings highlight that, beyond environmental filtering, plant genotype contributes to root microbiome assembly, offering perspectives for improving agricultural resilience through genotype-informed microbiome management. • We compared the root and rhizosphere microbiomes of five rye plant genotypes. • Root microbiomes differed significantly between local and modern varieties. • Genotype influence was evident in the most abundant endosphere ASVs • Landraces exhibit the capacity to recruit unique microbiomes in different ecosystems. • The assembly of the microbiome is influenced by plant-microbe-environment adaptation.