Fine‐Scale Temporal Dynamics of the Honey Bee Hive Microbiome and Foraging Revealed by Airborne eDNA

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ABSTRACT Environmental DNA (eDNA) has the potential to provide a rapid and non‐invasive screening approach for both honey bee health and foraging behavior. Here, we use eDNA carried in the air within honey bee colonies to analyze fine‐scale temporal patterns of foraging and microbial health, across both seasonal and diel scales. We identified nearly 100 genera of plants and more than 700 bacteria and fungi genera, including the core honey bee gut microbiome almost consistently detected in all samples. We detected wild, ornamental and cultivated plants supporting existing literature on honey bee generalist foraging behavior in urban environments. While overall richness of plant and microbiome remained stable throughout the active season (May to September), plant community composition varied significantly across months, likely reflecting seasonal turnover in local floral resources. At a finer diel scale, nor plant or microbiome richness and composition showed a significant day‐night differences, despite a trend of higher microbiome richness at night, potentially reflecting the accumulation of diverse microbiota from plants brought back in the hive by returning foragers and increased activity within the hive. These results demonstrate how airborne eDNA collected inside the bee hive can provide information on bee health and measure ecological data on a fine temporal scale to provide novel insights into bee ecology.

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