Study of the Metatranscriptome of Eight Social and Solitary Wild Bee Species Reveals Novel Viruses and Bee Parasites.

Karel Schoonvaere,Dirk C De Graaf,Guy Smagghe,Frédéric Francis

doi:10.3389/fmicb.2018.00177

Karel Schoonvaere, Dirk C De Graaf + Show 2 more

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https://doi.org/10.3389/fmicb.2018.00177

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Abstract

Bees are associated with a remarkable diversity of microorganisms, including unicellular parasites, bacteria, fungi, and viruses. The application of next-generation sequencing approaches enables the identification of this rich species composition as well as the discovery of previously unknown associations. Using high-throughput polyadenylated ribonucleic acid (RNA) sequencing, we investigated the metatranscriptome of eight wild bee species (Andrena cineraria, Andrena fulva, Andrena haemorrhoa, Bombus terrestris, Bombus cryptarum, Bombus pascuorum, Osmia bicornis, and Osmia cornuta) sampled from four different localities in Belgium. Across the RNA sequencing libraries, 88–99% of the taxonomically informative reads were of the host transcriptome. Four viruses with homology to insect pathogens were found including two RNA viruses (belonging to the families Iflaviridae and Tymoviridae that harbor already viruses of honey bees), a double stranded DNA virus (family Nudiviridae) and a single stranded DNA virus (family Parvoviridae). In addition, we found genomic sequences of 11 unclassified arthropod viruses (related to negeviruses, sobemoviruses, totiviruses, rhabdoviruses, and mononegaviruses), seven plant pathogenic viruses, and one fungal virus. Interestingly, nege-like viruses appear to be widespread, host-specific, and capable of attaining high copy numbers inside bees. Next to viruses, three novel parasite associations were discovered in wild bees, including Crithidia pragensis and a tubulinosematid and a neogregarine parasite. Yeasts of the genus Metschnikowia were identified in solitary bees. This study gives a glimpse of the microorganisms and viruses associated with social and solitary wild bees and demonstrates that their diversity exceeds by far the subset of species first discovered in honey bees.

Highlights

Transcriptomics is the study of all ribonucleic acid (RNA) molecules in a biological sample (Wang et al, 2009)
The transcriptome completeness was similar to an independent RNA-Seq study of B. terrestris queens (Harrison et al, 2015) indicating that around 70% transcriptome completeness is generally achieved for this caste and sequencing method
Since we initially identified fulllength VP and NS densoviral Open reading frames (ORFs) in two Bcry3 transcripts that could not be linked by paired-end RNA-Seq read data (Figure 2A), we anticipated a non-overlapping, ambisense genome organization similar to that of Diaphorina citri densovirus (DcDNV)

Summary

Introduction

Transcriptomics is the study of all ribonucleic acid (RNA) molecules in a biological sample (Wang et al, 2009). Depending on the extraction source, NGS data often comprise a mixture of reads from different species, that is, the host and its co-inhabiting (micro)organisms and viruses (Whitacre et al, 2015). This is notable when the source includes the digestive system (Douglas, 2015) or a specific tissue wherein symbionts reside (DeLay et al, 2012). Metatranscriptomics studies in bees are limited in number and most are dedicated to the domesticated honey bee, Apis mellifera These studies include investigations of the gut microbiome function (Lee et al, 2015), host-parasite interactions, and viral metagenomics (Runckel et al, 2011; Schoonvaere et al, 2016; Remnant et al, 2017) or both (Cox-Foster et al, 2007; Tozkar et al, 2015)

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