Fungal leaf endophytes play an important role in modulating host plant disease severity in Populus sp. Despite this, very little is known about the mechanisms that control endophyte community composition within a leaf. Examination of controls on community assembly of endophytes is crucial for optimization of integrative pest management methodologies for this economically important tree crop. We investigated how host genotype influences foliar fungal community structure in a fully factorial common garden experiment that included 12 Populus genotypes. In particular, we selected genotypes that varied in tannin concentrations, phenology, and resistance to a common Melampsora rust pathogen to determine whether these particular genotype-linked traits affect fungal community structure. Additionally, we attempted to induce community changes by implementing an herbivory treatment and an inoculation treatment (a common Cladosporium endophyte). Specifically, we are asking the following: 1) in a shared environment, is there a hierarchy of influence whereby genetic impacts are more influential than manipulative stressors (herbivory and inoculation treatments) in structuring fungal foliar endophytes and if so, is this hierarchy driven by the selected traits? And, 2) can we identify endophytic taxa associated with certain genotypes that would suggest fungal-host genetic linkages, and host filtering from the regional propagule pool.
Results/Conclusions
Using locus-targeted (fungal ITS1) Illumina MiSeq sequencing, we show that phenology and tannin levels play significant roles in structuring the foliar endophyte community (Bray-Curtis based iteratively sub-sampled PERMANOVA analysis), whereas herbivory, endophyte inoculation, and rust susceptibility showed no statistically significant effect on community composition. However, variance partitioning methods (PVCA) show that the significant genotype-linked traits that influence foliar communities are almost completely driven by genotype interactions, and host genotype alone is by far the most influential driver of fungal community structure. This result suggests that genetically-linked traits other than those that we measured influenced foliar fungal communities. Further, using LEfSe tests for taxa specificity, we identify several common taxa (mostly pathogens) that are significantly more abundant in one genotype providing targets for downstream genetic mapping efforts. This work demonstrates that investigating the genetic architecture of host plants is crucial for elucidating mechanisms of foliar community assembly.