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Title: Metatranscriptomic analyses of honey bee colonies

item TOZKAR, OZGE - Middle East Technical University
item KENCE, MERAL - Middle East Technical University
item KENCE, AYKUT - Middle East Technical University
item HUANG, QIANG - University Of Halle
item Evans, Jay

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2015
Publication Date: 8/20/2015
Citation: Tozkar, O.C., Kence, M., Kence, A., Huang, Q., Evans, J.D. 2015. Metatranscriptomic analyses of honey bee colonies. Frontiers in Genetics. doi: 10.3389/fgene.2015.00100.

Interpretive Summary: Honey bees are under attack by a diverse set of parasites and pathogens. A first goal to managing these disease agents is to assess each threat and determine which are most important for bee colony losses. This assessment can now be done using genomic resources for honey bees and all of the microbes and parasites found in association with bees and colonies. Here we describe this approach, using data from healthy and failing bee hives from across Turkey, a country with extensive honey bee management. The results give new insights into pathogens tied to bee losses, helping to direct research on improving bee health. They also provide researchers and regulators with a comparative data set between the US and another major beekeeping country, allowing comparative analyses of common bee threats.

Technical 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 5 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. 60 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, Apis filamentous 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.