Characterization of the Humulus lupulus microbiome for the biocontrol of phytopathogenic fungi: an eco-friendly solution for the Italian hop cultivation

Hop (Humulus lupulus L.) is a dioecious plant belonging to the Cannabaceae family. It naturally grows in temperate regions, but it is also cultivated for its secondary metabolites, which contribute flavor, bitterness, aroma, and antimicrobial properties to beer. Over 1,000 chemical compounds have been identified in hops, mainly essential oils, α- and β-acids, and prenylflavonoids. These compounds accumulate in the resinous substance called lupulin, found in the female flowers known as cones. In Europe, the main hop production areas are in the northeastern regions. However, in recent decades, cultivation has expanded toward southern European countries, including Italy. Despite the natural occurrence of hop plants across the Italian peninsula, this country still relies heavily on imports. Nonetheless, interest in local hop cultivation is growing, driven by the increasing number of microbreweries producing craft beers with unique flavors and tastes that favor locally grown hops over imported ones. One of the main challenges for developing hop cultivation in Italy is the lack of experience and knowledge about best practices, especially considering the specific climatic conditions of the Mediterranean. These conditions pose particular threats, such as phytopathogenic fungi like Pseudoperonospora humuli and Podosphaera macularis, along with other pests. Currently, management strategies mainly involve resistant cultivars and fungicides. However, the use of chemical treatments faces environmental concerns and regulatory limitations, such as the lack of registered active substances for hops under Italian legislation. An eco-friendly and sustainable alternative involves the use of plant endophytic fungi (Riccioni et al 2025), which can enhance plant health through various mechanisms—ranging from biological control of pathogens to biofertilization and stress tolerance. We first isolated, in pure cultures, endophytic fungi from both cultivated hops (cv. Cascade) and nearby wild hop sites in Central Italy with the aim to identify them taxonomically for future bioactivity testing against agronomically important phytopathogenic fungi. Since soil-borne pests are a major concern, we focused on endophytes from belowground parts of the plant—roots and rhizosphere. Our second goal was to characterize the microbiome (fungi and bacteria) of hop rhizosphere, roots, and cones, comparing cultivated and wild sites. This information will help in developing synthetic microbial communities to improve crop quality and disease resistance. For this activity, we used a metabarcoding approach, employing 16S rDNA and ITS markers to identify bacteria and fungi, respectively, along with a third-generation sequencing technology (MinION by Oxford Nanopore Technologies). Data analysis is ongoing to provide detailed insights into the species composition across different tissues and sampling sites.