Characterization of Foliar Fungal Endophyte Communities from White Pine Blister Rust Resistant and Susceptible Pinus flexilis in Natural Stands in the Southern Rocky Mountains

Fungal endophytic communities in needles of field-grown Pinus flexilis previously inferred to carry major gene resistance (R) to white pine blister rust (WPBR) or to lack it (S) were surveyed to identify unique microbes that may be recruited by WPBR-resistant genotypes. Resistant and susceptible trees were sampled in each of 11 P. flexilis populations for a total of 50 trees sampled. Through next-generation sequencing, this study showed a diverse needle mycobiota in P. flexilis, of which many remain unknown, regardless of the presence or absence of the WPBR resistance gene, Cr4. Ascomycota dominated the mycobiota (88.9%) followed by Basidiomycota (4.4%) and Chytridiomycota (0.03%), and the remaining 6.7% were unclassified. Shared (n = 105) and unique (n = 48 in R and n = 49 in S) fungal taxa, including differentially abundant operational taxonomic units, were identified that could provide insights into core mycobiota and host genotype-specific fungal groups. Marginal variation of the fungal diversity and structure was observed between host genotypes, which indicates that neither Cr4 nor the physiological differences associated with the presence or absence of the gene affects mycobiota recruitment. Instead, other parameters, including host size (diameter at breast height) and site elevation, significantly influenced the variability of the composition and structure of the fungal endophytic community. Further investigations are needed to understand the relationship of unique or differentially abundant taxa with one genotype or the other, and to determine the role of the needle mycobiota in WPBR disease development in natural stands of P. flexilis.