Foliar fungal endophytes form a ubiquitous, yet asymptomatic microbiome across all plant hosts studied to date. Fungal endophytes are increasingly being used as a model system for asking basic ecological and evolutionary questions about the structure and maintenance of host-associated, microbial communities. Phylogenetic distance among host species could represent a useful proxy for host traits that act as biotic filters on fungal endophyte colonization and persistence within leaf tissues. However, teasing apart biotic from abiotic assembly mechanisms in these hyperdiverse, horizontally-transmitted communities remains a challenge. In this study, we tested whether host phylogenetic relatedness and spatial distance between host individuals drives fungal endophyte community assembly. We used a novel common garden approach, to control for confounding factors such as host developmental age, seasonality, and regional-scale changes in climatic conditions. Specifically, replicate seedlings corresponding to 18 species from the plant family Asteraceae and one outgroup species from the sister family Lobeliaceae (Lobelia cardinalis) were planted in a common garden. After three months of exposure to natural inoculum, we collected and surface-sterilized leaves, and directly sequenced endophyte communities using an Illumina platform. A single locus phylogeny was reconstructed for the 19 host species using plant nuclear internal transcribed spacer sequences.
Overall, fungal endophyte community structure varied significantly among host species and marginally among plots within the common garden. Pairwise distance between individual host endophyte communities in ordination space was significantly predicted by the pairwise phylogenetic distance between host species, such that more closely related hosts shared more similar endophyte communities. Similarly, host individuals that were more spatially proximate in the common garden shared more similar fungal endophyte communities than more spatially distant hosts, though the magnitude of the spatial effect was weaker than the host phylogenetic effect. These results demonstrate an important role for biotic filters and host evolutionary relationships in shaping the endophyte microbiome, even when controlling for other mechanistic drivers, such as host age and regional environmental variation. Additionally, this study is the first to characterize the fungal endophyte microbiomes of many previously unexplored native Asteraceae in the Midwestern US.