Geographical and Seasonal Analysis of the Honeybee Microbiome.

We previously showed that colonies of thriving and non-thriving honeybees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here, we profiled the microbiome in returning forager bees from 10 to 12 hives in each of 6 apiaries across the southern half of Ireland, at early, middle, and late time points in the 2019 honey production season. Despite the wide range of geographical locations and forage available, apiary site was not the strongest determinant of the honeybee microbiome. However, there was clear clustering of the honeybee microbiome by time point across all apiaries, independent of which apiary was sampled. The clustering of microbiome by time was weaker although still significant in three of the apiaries, which may be connected to their geographic location and other external factors. The potential forage effect was strongest at the second timepoint (June-July) when the apiaries also displayed greatest difference in microbiome diversity. We identified bacteria in the forager bee microbiome that correlated with hive health as measured by counts of larvae, bees, and honey production. These findings support the hypothesis that the global honeybee microbiome and its constituent species support thriving hives.

Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs.

BACKGROUND: With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative SNPs for ancestry inference. RESULTS: Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. CONCLUSIONS: The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.

Pathogen prevalence in commercially reared bumble bees and evidence of spillover in conspecific populations.

Worldwide, wild bumble bees (Bombus spp.) are experiencing marked declines, with potentially up to 11% of species currently under threat. Recent studies from North America suggest that disease transmission from commercially reared bumble bees to wild populations has led to marked range contractions in some species. In Europe, data on the prevalence of pathogen spillover from commercial to wild bumble bee populations is lacking, despite the widespread production and transport of hives within the EU since the early 1980s. We determined the permeability of cropping systems to commercial bumble bees, and quantified the prevalence of four pathogens in commercial Bombus terrestris hives and adjacent conspecific populations at increasing distances from greenhouses in Ireland. Commercial bumble bees collected from 31% to 97% of non-crop pollen, depending on the cropping system, and hives had markedly higher frequencies of two gut parasites, Crithidia spp. and Nosema bombi, compared to adjacent populations, but were free of tracheal mites. The highest prevalence of Crithida was observed within 2 km of greenhouses and the probability of infection declined in a host sex- and pathogen-specific manner up to 10 km. We suggest implementing measures that prevent the interaction of commercially reared and wild bumble bees by integrating the enforcement of national best management practices for users of commercial pollinators with international legislation that regulates the sanitation of commercial hives in production facilities.