Cranberry Fungal Endophyte Presence in Cranberry Propagative Cuttings and Young Plantings From Central and Northern Wisconsin

Endophytic fungi are an understudied component of the cranberry microbiome, particularly within propagative plant material used to establish new plantings. This study characterised fungal endophytes from cranberry propagative tissue during two consecutive seasonal periods from commercial farms in Wisconsin, United States, including taxa that overlap with genera known to contain species associated with the cranberry fruit rot (CFR) complex. Fungal isolation and identification were conducted on plant samples obtained from nine farms and included vines from propagative bales stored for different durations and vines and berries from beds less than 3 years old. A total of 15,224 fungal colonies were counted across 1546 samples, with 904 isolates selected for identification. ITS sequencing confirmed seven fungal genera: Allantophomopsis , Coleophoma , Colletotrichum , Godronia , Phomopsis , Phyllosticta and Physalospora . Fungal colony counts were analysed using a generalised linear mixed model (GLMM) revealing significant year‐to‐year variation in fungal prevalence across tissue types and farms. This analysis highlighted tissue‐specific fungal distribution, with Phyllosticta spp. predominantly present in leaves, while Phomopsis spp. and Godronia spp. were more prevalent in lignified tissues. Understanding fungal prevalence across different tissue types and seasonal periods may inform our knowledge of fungal life cycles and potential transmission routes. This work should provide a foundation for future studies to evaluate which endophytes are associated with CFR development. While the fungal genera identified in this study overlap with those implicated in the CFR complex, their ecological roles and potential contributions to disease development remain unclear.