Seed‐derived microbiota in the Medicago holobiont: Associations with host phylogeny and breeding‐associated traits

Seed microbiota occupy unique ecological niches within plants and can form intimate associations with their hosts. However, how seed‐derived microbial communities are related to host phylogeny and breeding‐associated traits across natural and agricultural contexts, and whether trait‐associated microorganisms influence plant performance, remain poorly understood.

Here, we characterized endophytic communities in sterile‐grown seedlings from surface‐sterilized seeds of 10 wild Medicago genotypes representing 8 species and 20 domesticated alfalfa cultivars spanning multiple breeding decades. We assessed phylosymbiosis in wild hosts, examined associations between microbial community composition and breeding‐related cultivar characteristics in domesticated alfalfa, and constructed trait‐associated bacterial synthetic communities (SynComs) for functional evaluation.

In wild Medicago , bacterial, but not fungal, community composition exhibited significant congruence with host phylogeny, consistent with phylosymbiosis. In domesticated alfalfa, bacterial community composition was associated with cultivar trait category (high‐yielding vs. stress‐resistant), whereas fungal communities were not. Six cultivable candidate bacterial strains associated with the two trait categories were assembled into two SynComs, SynComY (high‐yielding associated) and SynComR (stress‐resistance‐associated). In vitro assays revealed multiple plant growth‐promoting and stress‐tolerance capacities among the constituent strains, while greenhouse experiments showed that SynComY promoted plant growth and SynComR enhanced plant performance under combined drought–salinity stress.

Synthesis . Together, these findings show that seed‐derived bacterial community structure is associated with host phylogeny in wild Medicago and breeding‐related trait differentiation in cultivated alfalfa, and further establish that selected bacteria associated with the latter can influence plant performance. Viewed within a holobiont framework, this combined evidence broadens our understanding of seed‐derived microbiota across natural and agricultural contexts and highlights their potential value for microbiome‐informed crop improvement.