Host species identity in annual Brassicaceae has a limited effect on the assembly of root-endophytic fungal communities

Background: Establishing the contribution of host plant genotype to the assembly of root-associated microbial communities can be challenging, since multiple ecological factors may confound the effects purely due to the host, and plant species often do not occur sympatrically. Aims: We aimed to measure the relative importance of host plant species on driving the assembly of natural root-endophytic fungal communities, as compared to other habitat conditions that depend on the local environment. Methods: Species of annual wild Brassicaceae and the cultivated Brassica napus were collected in two separate locations, where they grew in close proximity. Arrhentherum elatius (Poaceae) was also collected in both sites and used as outgroup. The root-endophytic fungal communities of these plants were characterised using Illumina MiSeq amplicon sequencing and cultivation, and compared between locations and hosts. Results: Plant family and sampling location were the factors driving most variation in fungal communities, affecting both community composition and the proportion of cultivable fungi. Whether Brassicaceae were wild or domesticated had little effect on endophytic communities, although its contribution increased when cultivable fungi were considered. No strong specificity of endophytes towards hosts was found, because a core mycobiome was shared by different species. Conclusions: Plant species is a limited predictor of the structure and composition of fungal endophytic communities in roots of annual Brassicaceae, as compared to geographic location. However, the host effect on endophytic assemblages increases with phylogenetic distance between hosts.