The almond bark beetle mycobiome: fungal associates of Scolytus amygdali within southern Mediterranean almond orchards

Bark beetles are fundamental drivers of forest ecosystem dynamics. However, some species within this group have recently also emerged as significant pests in environments managed by humans, including nurseries, orchards, and urban areas. Specifically, certain Scolytus species pose potential economic and ecological threats to stone fruit cultivation across the Mediterranean basin. Although the role of the mycobiome in mediating bark beetle–host interactions has been well documented for many forest models, the symbiotic associations between beetles and fungi in cultivated Mediterranean agroecosystems remain poorly understood. This study provides the first comprehensive characterization of the fungal community associated with the almond bark beetle Scolytus amygdali in southern Mediterranean almond orchards. Integrating culture-dependent isolations with culture-independent approaches, i.e., high-throughput sequencing, allowed us to assess the beetle mycobiome across beetle adults, gallery systems, and associated necrotic wood lesions. Molecular characterization revealed Geosmithia, Paecilomyces, and Quambalaria to be the dominant taxa within the S. amygdali mycobiome. Their frequent occurrence suggests that they may be recurrent associates in the gallery environment, although their functional roles remain unclear. Furthermore, metabarcoding analyses provided additional novel insights into the beetle mycobiome, identifying Candida and Yamadazyma yeasts as potential core constituents of the gut microbiome. Future research should prioritize elucidating the role of these putative fungal symbionts for the beetles, particularly the pathogenic potential on almonds, and the functional efficiency of S. amygdali as a vector. Overall, our findings elucidate the complex taxonomic diversity of these associations. Moreover, obtained results provide a foundational ecological framework to better understand to what extent these associations can threaten host plants and to develop future sustainable management strategies in managed ecosystems.