Temporal Changes in Fungal and Bacterial Communities in Developing Hop Cones and Rhizomes Over a Single Growing Season

Hops are a culturally and economically important crop with centuries of use. The primary harvested component is the hop cone (female flower), which undergoes physiological and chemical changes during development. To better understand the relationship between developing hop cones and their associated microbes, this study utilized amplicon-based sequencing of the internal transcribed spacer 1 (ITS1) and the 16S regions to characterize the associated fungal and bacterial communities, respectively. By sampling developing cones (i.e. bract or burr tissues) across ten successive weeks, as well as rhizomes the following year, this study presents a preliminary profiling of the hop cone and rhizome microbial communities. Fungal diversity of the hop cone was found to vary throughout development (R 2 = 0.37, p < 0.0001), with diversity decreasing concomitant with the emergence of Diaporthe humulicola. Both fungal and bacterial communities varied between cones and rhizome, with a more variation in composition between tissues being observed in the bacterial communities (fungal: R 2 = 0.14, bacterial: R 2 = 0.24, p < 0.0001). A core microbiome across the weekly sampling of the hop cone and tissue types was identified for both the fungal and bacterial communities, with Alternaria, Diaporthe, and Vishniacozyma species among the fungal core microbiome and Pseudomonas, Pantoea, and Sphingomonas species among the bacterial. This work provides novel insights into the temporal patterns of the hop cone microbiome and the hop rhizome microbiome, as well as the observation of the emerging hop pathogen Diaporthe humulicola potentially reducing the abundance of other fungi in the hop cone.