Transmission mode and assembly of seed fungal endophyte communities in wheat and wheat wild relatives

Seeds acquire fungal endophytes either from the environment or from their progenitors. These transmission modes are central in shaping the microbiome as they affect species composition and balance. We studied fungal endophyte communities (FEC) in three plant species: bread wheat (Triticum aestivum), wild emmer wheat (Triticum turgidum dicoccoides), and wild barley (Hordeum spontaneum). We conducted two experiments to test seed-to-seed transmission: (i) we compared FECs in stems and seeds collected from agricultural and natural habitats, and (ii) we grew plants under greenhouse conditions to isolate the effect of vertical transmission on the plant FECs. The analysis of seed communities revealed differences in FEC composition and diversity among plant species; however, Alternaria infectoria dominated FECs in all plant species. In field-collected plants, the number of taxa in the seeds was less than half the number in stems, and close to 90% of the seed taxa were found in stems. The FECs from stems and seeds of greenhouse-grown plants were more diverse than the FECs of original seeds; they lacked a single dominant taxon, and new seeds FECs had a similar richness and diversity to stems FECs, with only 40% overlap. The controlled environment experiment confirmed vertical transmission of certain species but also showed that external infection of the seeds is the main source for specific taxa. Our results show that many taxa can reach the seeds internally, albeit in different abundance, that both infection sources affect seed FECs composition, and that external conditions the balance between FECs within the plant.