Viral Diversity in Mixed Tree Fruit Production Systems Determined through Bee-Mediated Pollen Collection

Commercially cultivated <i>Prunus</i> species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (<i>Malus domestica</i>), another member of the <i>Rosacea</i> and distantly related to <i>Prunus</i>, can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites. Commercial honey bee (<i>Apis mellifera</i>) pollination is essential for improved fruit sets and yields in tree fruit production systems. To better understand the pollen-associated virome in tree fruits, metagenomics-based detection of plant viruses was employed on bee and pollen samples collected at four time points during the peak bloom period of apricot, cherry, peach, and apple trees at one orchard site. Twenty-one unique viruses were detected in samples collected during tree fruit blooms, including prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV) (Genus <i>Ilarvirus</i>, family <i>Bromoviridae</i>), <i>Secoviridae</i> family members tomato ringspot virus (genus <i>Nepovirus</i>), tobacco ringspot virus (genus <i>Nepovirus</i>), prunus virus F (genus <i>Fabavirus</i>), and <i>Betaflexiviridae</i> family member cherry virus A (CVA; genus <i>Capillovirus</i>). Viruses were also identified in composite leaf and flower samples to compare the pollen virome with the virome associated with vegetative tissues. At all four time points, a greater diversity of viruses was detected in the bee and pollen samples. Finally, the nucleotide sequence diversity of the coat protein regions of CVA, PDV, and PNRSV was profiled from this site, demonstrating a wide range of sequence diversity in pollen samples from this site. These results demonstrate the benefits of area-wide monitoring through bee pollination activities and provide new insights into the diversity of viruses in tree fruit pollination ecosystems.