Corylus avellana Disease Management: Using Metagenomics to Illuminate the Rhizosphere Microbiome of Hazelnut

The European hazelnut, Corylus avellana, is an economically important tree nut crop. The biotrophic ascomycete pathogen Anisogramma anomala, found naturally associated with wild C. americana, continues to pose a significant threat to European hazelnut production across North America. Here, metagenomics was used to examine the taxonomic and functional features of the rhizosphere microbial communities of hazelnut trees differing in their A. anomala disease phenotypes: non-symptomatic Corylus americana, and non-symptomatic and symptomatic Corylus avellana. No statistically significant differences in microbial alpha diversity or beta diversity were noted between the three rhizosphere groups. Compared to bulk soil, all three rhizosphere groups were enriched for the fungal phylum Basidiomycota and bacterial phylum “Candidatus Rokubacteriota”. At the genus level, the bacterial genera Actinospica, Occallatibacter, and “Candidatus Sulfotelmatobacter” were under-represented, while the genus Rhizobacter was over-represented in the non-symptomatic and symptomatic C. avellana rhizosphere samples compared to the bulk soil. A total of 45 dereplicated, high-quality metagenome-assembled genomes (MAGs) were generated, corresponding to 41 bacteria and 4 archaea. Many of the MAGs carried multiple biosynthetic gene clusters, including MAGs corresponding to the genera Lysobacter and Actinospica. Overall, the low differentiation of the rhizosphere microbiomes suggest that differences in A. anomala disease expression are likely not associated with stable, year-round differences in the rhizosphere microbiome. Nevertheless, the results shed new light on the rhizosphere communities of two species of hazelnut, and woody perennials more broadly, and identify potential avenues for future research into the development of microbial inoculants for Corylus species.