Characterisation of the UK honey bee (Apis mellifera) metagenome

Abstract

The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of a pathogenic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.

Trypanosomatid parasite dynamically changes the transcriptome during infection and modifies honey bee physiology

“…Recently, a novel trypanosomatid parasite was discovered and named L. passim 7 . L. passim seems to be more prevalent than C. mellificae [7][8][9][10][11][12][13][14][15][16][17][18] . Although the association of L. passim infection with winter mortality of honey bee colonies was suggested in several studies 19,20 , the effects of L. passim infection on honey bee health and colony survival remain poorly understood.…”

Gene Disruption of Honey Bee Trypanosomatid Parasite, Lotmaria passim, by CRISPR/Cas9 System

“…Later, in 2015, another novel trypanosomatid parasite infecting honey bees was discovered and named L. passim (Schwarz et al, 2015). L. passim was found to be more prevalent than C. mellificae (Schmid-Hempel and Tognazzo, 2010; Morimoto et al, 2013; Cepero et al, 2014; Ravoet et al, 2014, 2015; Cersini et al, 2015; Schwarz et al, 2015; Arismendi et al, 2016; Cavigli et al, 2016; Stevanovic et al, 2016; Vavilova et al, 2017; Regan et al, 2018) and fewer honey bee colonies were reported to be infected by C. mellificae (Ravoet et al, 2015). Thus, L. passim rather than C. mellificae is likely to be associated with the previously reported winter mortality of honey bee colonies (Ravoet et al, 2013).…”

Protocols for assessing the distribution of pathogens in individual Hymenopteran pollinators

“…Although these protocols are designed around bees and their shared pathosphere [28][29][30][31] , they can easily be adapted to other groups of organism with common pathogens and distributions. The protocols are based on the detection and quanti cation of pathogen nucleic acid in a sample, rather than the disease consequences of the presence and loads of these pathogens for individual bee species 18 .…”