Spatiotemporal variation in honeybee ( Apis mellifera L.) virome composition across landscape types and seasons

Honeybees face increasing threats from biotic stress of viral pathogens that can severely impact colony health and contribute to global colony decline. However, comprehensive studies of biotic stress and composition of bee viruses across different environmental contexts and seasons remain scarce. This study aims to characterize and compare the diversity, abundance and composition of the Apis mellifera L. virome across three different landscapes (conventional, organic, and roadside) and seasonal gradients (early vs. late season) to better understand how environmental and temporal factors affect viral communities in honeybees. A. mellifera were collected from three different habitats (conventional farm, organic farm, and roadside habitat) during the spring and summer of 2024. Total RNA was extracted individually from whole honeybees and mRNA libraries were prepared, which were subsequently used for sequencing on an Illumina NovaSeq X Plus platform using paired-end 150 bp reads. Several bacteriophages, putative novel viruses, plant-, insect- and bee-associated viruses were detected in the honeybee viromes including Sacbrood virus, Black queen cell virus, Deformed wing virus-B (previously known as Varroa destructor virus-1) and Deformed wing virus. Furthermore, both habitat types and seasons influence viral abundance as majority of detected viruses showed higher abundance in the conventional farm and late season samples. The present findings provide novel insights into the ecological and seasonal dynamics of honeybee-virus interactions and contribute to strategies for improving honeybee health and resilience.