Beekeeping operation-level virus complexes rather than specific viruses are associated with increased colony mortality in underperforming beekeeping operations. 2023; in preparation.

Honey bees are principal managed pollinators and their increased losses pose a threat to global agriculture. Significant variation in the rates of colony losses could be observed even within the same geographical regions, and the factors affecting honey bee colony survival are not fully understood. To investigate whether microbes and Varroa parasite affect survival of individual colonies and overall apiary performance, we conducted a longitudinal observational study, which continued from June 2018 to February 2019 and involved 144 colonies in three pairs of apiaries with contrasting levels of historic colony losses located in the US states of Oregon, Michigan and North Dakota. The observed apiary colony losses during 8 month observation ranged from 8% to 100% months, and were significantly higher in historically underperforming apiaries compared to the well-performing in each state. Varroa infestation levels, which peaked in October, were also higher in the underperforming apiaries. Metagenomic analysis of the honey bees was carried out at two time points, in June and October 2018, with the aims to investigate geographical and temporal variation of microbial communities, and to compare colonies which died or survived within the next 4 months. This analysis showed that the presence of distinct microbial complexes in each of the six apiaries in June and October, and the colonies from the same apiaries which died or survived had similar microbiomes. Composition of virus complexes showed stronger changes between June to October compared to other microbes, and common season-specific features of virus complexes observed for all apiaries. Analysis of the colony-level loads of the most prevalent viruses, showed that while different virus complexes were observed in the apiaries with various levels of colony losses, there were no single virus or virus complex strongly associated with the survival of individual colonies with apiary.