Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia

TLDR

Honey bees are essential pollinators, yet their populations in North America and Europe have suffered unexplained losses known as Colony Collapse Disorder, a problem hampered by a lack of comprehensive pathogen studies. The study aimed to define abnormal colony health by characterizing the full spectrum of exogenous infectious agents present in healthy hives over time. Researchers conducted a prospective survey of a large migratory beekeeping operation, employing high‑frequency sampling coupled with custom microarray, qPCR, and ultra‑deep sequencing to detect pathogens. Seasonal monitoring showed that common viruses and Nosema peaked in summer, while Crithidia mellificae and Lake Sinai virus 2 peaked in January, and ultra‑deep sequencing identified four novel RNA viruses, two of which were the most abundant constituents of the honey‑bee microbiome.

Abstract

Honey bees (Apis mellifera) play a critical role in global food production as pollinators of numerous crops. Recently, honey bee populations in the United States, Canada, and Europe have suffered an unexplained increase in annual losses due to a phenomenon known as Colony Collapse Disorder (CCD). Epidemiological analysis of CCD is confounded by a relative dearth of bee pathogen field studies. To identify what constitutes an abnormal pathophysiological condition in a honey bee colony, it is critical to have characterized the spectrum of exogenous infectious agents in healthy hives over time. We conducted a prospective study of a large scale migratory bee keeping operation using high-frequency sampling paired with comprehensive molecular detection methods, including a custom microarray, qPCR, and ultra deep sequencing. We established seasonal incidence and abundance of known viruses, Nosema sp., Crithidia mellificae, and bacteria. Ultra deep sequence analysis further identified four novel RNA viruses, two of which were the most abundant observed components of the honey bee microbiome (∼1011 viruses per honey bee). Our results demonstrate episodic viral incidence and distinct pathogen patterns between summer and winter time-points. Peak infection of common honey bee viruses and Nosema occurred in the summer, whereas levels of the trypanosomatid Crithidia mellificae and Lake Sinai virus 2, a novel virus, peaked in January.