Abstract
Honey bees face numerous biotic threats from viruses to bacteria, fungi, protists, and mites. Here we describe a thorough analysis of microbes harbored by worker honey bees collected from field colonies in geographically distinct regions of Turkey. Turkey is one of the World's most important centers of apiculture, harboring five subspecies of Apis mellifera L., approximately 20% of the honey bee subspecies in the world. We use deep ILLUMINA-based RNA sequencing to capture RNA species for the honey bee and a sampling of all non-endogenous species carried by bees. After trimming and mapping these reads to the honey bee genome, approximately 10% of the sequences (9–10 million reads per library) remained. These were then mapped to a curated set of public sequences containing ca. Sixty megabase-pairs of sequence representing known microbial species associated with honey bees. Levels of key honey bee pathogens were confirmed using quantitative PCR screens. We contrast microbial matches across different sites in Turkey, showing new country recordings of Lake Sinai virus, two Spiroplasma bacterium species, symbionts Candidatus Schmidhempelia bombi, Frischella perrara, Snodgrassella alvi, Gilliamella apicola, Lactobacillus spp.), neogregarines, and a trypanosome species. By using metagenomic analysis, this study also reveals deep molecular evidence for the presence of bacterial pathogens (Melissococcus plutonius, Paenibacillus larvae), Varroa destructor-1 virus, Sacbrood virus, and fungi. Despite this effort we did not detect KBV, SBPV, Tobacco ringspot virus, VdMLV (Varroa Macula like virus), Acarapis spp., Tropilaeleps spp. and Apocephalus (phorid fly). We discuss possible impacts of management practices and honey bee subspecies on microbial retinues. The described workflow and curated microbial database will be generally useful for microbial surveys of healthy and declining honey bees.
Highlights
The honey bee (Apis mellifera L.) has ecological importance as a natural pollinator of wild flora and crops
Read Mapping Results Deformed wing virus (DWV) reads were detected in sequenced RNA libraries from all of the regions (Figure 4 and Table 4 in Supplementary Material), they were most highly represented in Hatay, Yıgılca, and Mugla, matching the results from real time q-PCR
Consistent with the fact that Black queen cell virus (BQCV) was not detected in Yıgılca by RT-qPCR very few reads were found in this province during RNA sequencing According to the sequence analysis, Acute bee paralysis virus (ABPV) contigs were common in most regions
Summary
The honey bee (Apis mellifera L.) has ecological importance as a natural pollinator of wild flora and crops. Managed honey bees have economical importance with hive products including honey, pollen, wax, propolis, and royal jelly (Maheshwari, 2003). Declines of managed colonies have been noted on many continents Several causes of these large-scale losses have been reported, including honey bee parasites (Varroa destructor, Acarapis woodi); Honey bee microbial transcriptomics pathogens (Nosema spp. and bee viruses); pesticides, contaminated water, use of antibiotics, poor nutrition, and migratory beekeeping practices (Kevan et al, 2007; Higes et al, 2008; Naug, 2009; vanEngelsdorp et al, 2009; Bacandritsos et al, 2010; vanEngelsdorp and Meixner, 2010). We will focus on honey bee pathogens and parasites and the use of modern sequencing techniques to identify these agents in healthy and declining colonies
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