A survey of the microbiota of New Zealand hop (Humulus lupulus)

Abstract

Humulus lupulus (common hop) is a key ingredient for beer brewing, owing to the secondary compounds that accumulate in the inflorescence. Currently, New Zealand hop growers benefit from conducive climatic conditions, few pests and diseases, and an innovative breeding programme driven by increased demand for hop-forward beer. While genetic resources provide the foundations for novel cultivar development, import of new germplasm is currently bottlenecked by biosecurity regulations aimed at mitigating coimportation of pests and pathogens. Tissue culture (TC) has been recognised as a potential avenue to mitigate these risks, because of a reduced microbial diversity and its well-defined characteristics. Hops are easily propagated and provide an excellent model for investigating microbial colonisation and persistence in TC. However, little is known about the hop microbiome to provide the basis for these investigations. We conducted a survey of the bacterial and fungal communities from the rhizomes, leaves, and inflorescences of two New Zealand cultivars using DNA metabarcoding and culturing. Our analysis revealed bacterial and fungal communities structured by tissue type, with strong partitioning between above-ground and below-ground compartments. Heterogeneity among samples varied with tissue type and between bacteria and fungi, suggesting tissue-specific selection is met with different responses by the two key microbial groups. Within these communities, conserved bacterial genera from the different plant compartments, including Sphingomonas, Frigoribacterium, Curtobacterium, Varivorax, Luteibacter, and Streptomyces, were identified as initial candidates for TC recolonisation experiments. Upcoming experiments will focus on evaluating asymptomatic colonisation and persistence in TC, to better understand microbial co-importation risk.