Study of the metatranscriptome of eight social and solitary wild bee species reveals novel viruses and bee parasites

[en] 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. © 2018 Schoonvaere, Smagghe, Francis and de Graaf.

Disciplines :

Entomology & pest control

Author, co-author :

Schoonvaere, Karel ; Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Gestion durable des bio-agresseurs

Smagghe, G.; Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium

Francis, Frédéric ; Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Gestion durable des bio-agresseurs

de Graaf, D. C.; Laboratory of Molecular Entomology and Bee Pathology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium

Language :

English

Title :

Study of the metatranscriptome of eight social and solitary wild bee species reveals novel viruses and bee parasites

Publication date :

2018

Journal title :

Frontiers in Microbiology

eISSN :

1664-302X

Publisher :

Frontiers Media S.A.

Volume :

Issue :

FEB

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 13 December 2019

Statistics

Number of views

64 (1 by ULiège)

Number of downloads

42 (0 by ULiège)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

OpenCitations

Bibliography

Aufauvre, J., Misme-Aucouturier, B., Vigues, B., Texier, C., Delbac, F., and Blot, N. (2014). Transcriptome analyses of the honeybee response to Nosema ceranae and insecticides. PLOS ONE 9:e91686. doi: 10.1371/journal.pone.0091686
Brown, M. J. F. (2017). Microsporidia: an emerging threat to bumblebees? Trends Parasitol. 33, 754-762. doi: 10.1016/j.pt.2017.06.001
Brysch-Herzberg, M. (2004). Ecology of yeasts in plant-bumblebee mutualism in Central Europe. FEMS Microbiol. Ecol. 50, 87-100. doi: 10.1016/j.femsec.2004.06.003
Buchfink, B., Xie, C., and Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59-60. doi: 10.1038/nmeth.3176
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421. doi: 10.1186/1471-2105-10-421
Chang, J. M., Di Tommaso, P., and Notredame, C. (2014). TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Mol. Biol. Evol. 31, 1625-1637. doi: 10.1093/molbev/msu117
Cooper, J. I. (1979). Virus Diseases of Trees and Shrubs. Cambridge: Institute of Terrestrial Ecology
Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., et al. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318, 283-287. doi: 10.1126/science.1146498
Darriba, D., Taboada, G. L., Doallo, R., and Posada, D. (2011). ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164-1165. doi: 10.1093/bioinformatics/btr088
de Miranda, J. R., Bailey, L., Ball, B. V., Blanchard, P., Budge, G. E., Chejanovsky, N., et al. (2013). Standard methods for virus research in Apis mellifera. J. Apic. Res. 52, 1-56. doi: 10.3896/IBRA.1.52.4.22
de Miranda, J. R., Cornman, R. S., Evans, J. D., Semberg, E., Haddad, N., Neumann, P., et al. (2015). Genome characterization, prevalence and distribution of a macula-like virus from Apis mellifera and Varroa destructor. Viruses 7, 3586-3602. doi: 10.3390/v7072789
de Miranda, J. R., Hedman, H., Onorati, P., Stephan, J., Karlberg, O., Bylund, H., et al. (2017). Characterization of a novel RNA virus discovered in the autumnal moth Epirrita autumnata in Sweden. Viruses 9, 214. doi: 10.3390/v9080214
DeLay, B., Mamidala, P., Wijeratne, A., Wijeratne, S., Mittapalli, O., Wang, J., et al. (2012). Transcriptome analysis of the salivary glands of potato leafhopper, Empoasca fabae. J. Insect Physiol. 58, 1626-1634. doi: 10.1016/j.jinsphys.2012.10.002
Dhar, A. K., Robles-Sikisaka, R., Saksmerprome, V., and Lakshman, D. K. (2014). Biology, genome organization, and evolution of parvoviruses in marine shrimp. Adv. Virus Res. 89, 85-139. doi: 10.1016/B978-0-12-800172-1.00003-3
Dheilly, N. M., Maure, F., Ravallec, M., Galinier, R., Doyon, J., Duval, D., et al. (2015). Who is the puppet master? Replication of a parasitic wasp-associated virus correlates with host behaviour manipulation. Proc. Biol. Sci. 282:20142773. doi: 10.1098/rspb.2014.2773
Dolezal, A. G., Hendrix, S. D., Scavo, N. A., Carrillo-Tripp, J., Harris, M. A., Wheelock, M. J., et al. (2016). Honey bee viruses in wild bees: viral prevalence, loads, and experimental inoculation. PLOS ONE 11:e0166190. doi: 10.1371/journal.pone.0166190
Douglas, A. E. (2015). Multiorganismal insects: diversity and function of resident microorganisms. Annu. Rev. Entomol. 60, 17-34. doi: 10.1146/annurev-ento-010814-020822
Engel, P., Kwong, W. K., McFrederick, Q., Anderson, K. E., Barribeau, S. M., Chandler, J. A., et al. (2016). The Bee microbiome: impact on bee health and model for evolution and ecology of host-microbe interactions. mBio 7:e2164-15. doi: 10.1128/mBio.02164-15
Evans, J. D., and Schwarz, R. S. (2011). Bees brought to their knees: microbes affecting honey bee health. Trends Microbiol. 19, 614-620. doi: 10.1016/j.tim.2011.09.003
Gouy, M., Guindon, S., and Gascuel, O. (2010). SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221-224. doi: 10.1093/molbev/msp259
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652. doi: 10.1038/nbt.1883
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., and Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321. doi: 10.1093/sysbio/syq010
Harrison, M. C., Hammond, R. L., and Mallon, E. B. (2015). Reproductive workers show queenlike gene expression in an intermediately eusocial insect, the buff-tailed bumble bee Bombus terrestris. Mol. Ecol. 24, 3043-3063. doi: 10.1111/mec.13215
Huger, A. M. (1985). A new virus disease of crickets (Orthoptera: Gryllidae) causing macronucleosis of fatbody. J. Invertebr. Pathol. 45, 108-111. doi: 10.1016/0022-2011(85)90055-2
Huger, A. M. (2005). The Oryctes virus: its detection, identification, and implementation in biological control of the coconut palm rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae). J. Invertebr. Pathol. 89, 78-84. doi: 10.1016/j.jip.2005.02.010
Husband, R. W., and Shina, R. N. (1970). A revision of the genus Locustacarus with a key to the genera of the family Podapolipidae (Acarina). Ann. Entomol. Soc. Am. 63, 1152-1162. doi: 10.1093/aesa/63.4.1152
Huson, D. H., Auch, A. F., Qi, J., and Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome Res. 17, 377-386. doi: 10.1101/gr.5969107
Katoh, K., and Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780. doi: 10.1093/molbev/mst010
Katsuma, S., Tanaka, S., Omuro, N., Takabuchi, L., Daimon, T., Imanishi, S., et al. (2005). Novel macula-like virus identified in Bombyx mori cultured cells. J. Virol. 79, 5577-5584. doi: 10.1128/JVI.79.9.5577-5584.2005
Kim, D., Langmead, B., and Salzberg, S. L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357-360. doi: 10.1038/nmeth.3317
Koyama, S., Urayama, S., Ohmatsu, T., Sassa, Y., Sakai, C., Takata, M., et al. (2015). Identification, characterization and full-length sequence analysis of a novel dsRNA virus isolated from the arboreal ant Camponotus yamaokai. J. Gen. Virol. 96(Pt 7), 1930-1937. doi: 10.1099/vir.0.000126
Lachance, M. A. (2016). Metschnikowia: half tetrads, a regicide and the fountain of youth. Yeast 33, 563-574. doi: 10.1002/yea.3208
Lee, F. J., Rusch, D. B., Stewart, F. J., Mattila, H. R., and Newton, I. L. (2015). Saccharide breakdown and fermentation by the honey bee gut microbiome. Environ. Microbiol. 17, 796-815. doi: 10.1111/1462-2920.12526
Li, C. X., Shi, M., Tian, J. H., Lin, X. D., Kang, Y. J., Chen, L. J., et al. (2015). Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. Elife 4:e05378. doi: 10.7554/eLife.05378
Li, J. L., Cornman, R. S., Evans, J. D., Pettis, J. S., Zhao, Y., Murphy, C., et al. (2014). Systemic spread and propagation of a plant-pathogenic virus in European Honeybees, Apis mellifera. mBio 5:e898-13. doi: 10.1128/mBio.00898-13
Li, X., Xu, P., Yang, X., Yuan, H., Chen, L., and Lu, Y. (2017). The genome sequence of a novel RNA virus in Adelphocoris suturalis. Arch. Virol. 162, 1397-1401. doi: 10.1007/s00705-016-3211-2
Lipa, J. J., and Triggiani, O. (1996). Apicystis gen nov and Apicystis bombi (Liu, Macfarlane & Pengelly) comb nov (Protozoa: Neogregarinida), a cosmopolitan parasite of Bombus and Apis (Hymenoptera: Apidae). Apidologie 27, 29-34. doi: 10.1051/apido:19960104
Maebe, K., Meeus, I., Vray, S., Claeys, T., Dekoninck, W., Boeve, J. L., et al. (2016). A century of temporal stability of genetic diversity in wild bumblebees. Sci. Rep. 6:38289. doi: 10.1038/srep38289
Malysh, J. M., Tokarev, Y. S., Sitnicova, N. V., Martemyanov, V. V., Frolov, A. N., and Issi, I. V. (2013). Tubulinosema loxostegi sp. n. (Microsporidia: Tubulinosematidae) from the Beet Webworm Loxostege sticticalis L. (Lepidoptera: Crambidae) in Western Siberia. Acta Protozool. 52, 299-309. doi: 10.4467/16890027AP.13.028.1319
Martinez, J., Lepetit, D., Ravallec, M., Fleury, F., and Varaldi, J. (2016). Additional heritable virus in the parasitic wasp Leptopilina boulardi: prevalence, transmission and phenotypic effects. J. Gen. Virol. 97, 523-535. doi: 10.1099/jgv.0.000360
McMahon, D. P., Furst, M. A., Caspar, J., Theodorou, P., Brown, M. J., and Paxton, R. J. (2015). A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. J. Anim. Ecol. 84, 615-624. doi: 10.1111/1365-2656.12345
Nabeshima, T., Inoue, S., Okamoto, K., Posadas-Herrera, G., Yu, F., Uchida, L., et al. (2014). Tanay virus, a new species of virus isolated from mosquitoes in the Philippines. J. Gen. Virol. 95(Pt 6), 1390-1395. doi: 10.1099/vir.0.061887-0
Nigg, J. C., Nouri, S., and Falk, B. W. (2016). Complete genome sequence of a putative densovirus of the Asian citrus psyllid, Diaphorina citri. Genome Announc. 4:e589-16. doi: 10.1128/genomeA.00589-16
Oppenheim, S. J., Baker, R. H., Simon, S., and DeSalle, R. (2015). We can't all be supermodels: the value of comparative transcriptomics to the study of non-model insects. Insect Mol. Biol. 24, 139-154. doi: 10.1111/imb.12154
Peng, W. J., Li, J. L., Boncristiani, H., Strange, J. P., Hamilton, M., and Chen, Y. P. (2011). Host range expansion of honey bee black queen cell virus in the bumble bee, Bombus huntii. Apidologie 42, 650-658. doi: 10.1007/s13592-011-0061-5
Peters, R. S., Krogmann, L., Mayer, C., Donath, A., Gunkel, S., Meusemann, K., et al. (2017). Evolutionary history of the hymenoptera. Curr. Biol. 27, 1013-1018. doi: 10.1016/j.cub.2017.01.027
Pionar, G. O., and Van der Laan, P. A. (1972). Morphology and life history of Sphaerularia bombi. Nematologica 18, 239-252. doi: 10.1163/187529272X00476
Plischuk, S., Sanscrainte, N. D., Becnel, J. J., Estep, A. S., and Lange, C. E. (2015). Tubulinosema pampeana sp. n. (Microsporidia, Tubulinosematidae), a pathogen of the South American bumble bee Bombus atratus. J. Invertebr. Pathol. 126, 31-42. doi: 10.1016/j.jip.2015.01.006
R Development Core Team (2011). R: A Language and Environment for Statistical Computing. Available at: http://www.R-project.org/
Ravoet, J., De Smet, L., Meeus, I., Smagghe, G., Wenseleers, T., and de Graaf, D. C. (2014). Widespread occurrence of honey bee pathogens in solitary bees. J. Invertebr. Pathol. 122, 55-58. doi: 10.1016/j.jip.2014.08.007
Remnant, E. J., Shi, M., Buchmann, G., Blacquiere, T., Holmes, E. C., Beekman, M., et al. (2017). A diverse range of novel RNA viruses in geographically distinct honey bee populations. J. Virol. 91:e158-17. doi: 10.1128/JVI.00158-17
Riddell, C. E., Lobaton Garces, J. D., Adams, S., Barribeau, S. M., Twell, D., and Mallon, E. B. (2014). Differential gene expression and alternative splicing in insect immune specificity. BMC Genomics 15:1031. doi: 10.1186/1471-2164-15-1031
Runckel, C., Flenniken, M. L., Engel, J. C., Ruby, J. G., Ganem, D., Andino, R., et al. (2011). Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia. PLOS ONE 6:e20656. doi: 10.1371/journal.pone.0020656
Schmid-Hempel, R., and Tognazzo, M. (2010). Molecular divergence defines two distinct lineages of Crithidia bombi (Trypanosomatidae), parasites of bumblebees. J. Eukaryot. Microbiol. 57, 337-345. doi: 10.1111/j.1550-7408.2010.00480.x
Schoonvaere, K. (2017). Study of the virome of 8 wild bee species in Belgium. doi: 10.6084/m9.figshare.c.3902704.v1
Schoonvaere, K., De Smet, L., Smagghe, G., Vierstraete, A., Braeckman, B. P., and de Graaf, D. C. (2016). Unbiased RNA shotgun metagenomics in social and solitary wild bees detects associations with Eukaryote Parasites and New Viruses. PLOS ONE 11:e0168456. doi: 10.1371/journal.pone.0168456
Shi, M., Lin, X. D., Tian, J. H., Chen, L. J., Chen, X., Li, C. X., et al. (2016). Redefining the invertebrate RNA virosphere. Nature 540, 539-543. doi: 10.1038/nature20167
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., and Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210-3212. doi: 10.1093/bioinformatics/btv351
Singh, R., Levitt, A. L., Rajotte, E. G., Holmes, E. C., Ostiguy, N., Vanengelsdorp, D., et al. (2010). RNA Viruses in hymenopteran pollinators: evidence of inter-taxa virus transmission via pollen and potential impact on non-Apis hymenopteran species. PLOS ONE 5:e14357. doi: 10.1371/journal.pone.0014357
Sipiczki, M. (2006). Metschnikowia strains isolated from botrytized grapes antagonize fungal and bacterial growth by iron depletion. Appl. Environ. Microbiol. 72, 6716-6724. doi: 10.1128/AEM.01275-06
Smith, K. G. V. (1969). Diptera, Conopidae, Handbooks for The Identification of British Insects, Vol. 10. London: Royal Entomological Society
Szelei, J., Woodring, J., Goettel, M. S., Duke, G., Jousset, F. X., Liu, K. Y., et al. (2011). Susceptibility of North-American and European crickets to Acheta domesticus densovirus (AdDNV) and associated epizootics. J. Invertebr. Pathol. 106, 394-399. doi: 10.1016/j.jip.2010.12.009
Tange, O. (2011). GNU parallel-the command-line power tool. USENIX Mag. 36, 42-47. doi: 10.5281/zenodo.16303
Tokarz, R., Williams, S. H., Sameroff, S., Sanchez Leon, M., Jain, K., and Lipkin, W. I. (2014). Virome analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis ticks reveals novel highly divergent vertebrate and invertebrate viruses. J. Virol. 88, 11480-11492. doi: 10.1128/JVI.01858-14
Tozkar, C. O., Kence, M., Kence, A., Huang, Q., and Evans, J. D. (2015). Metatranscriptomic analyses of honey bee colonies. Front. Genet. 6:100. doi: 10.3389/fgene.2015.00100
Wang, Y., Bininda-Emonds, O. R., and Jehle, J. A. (2012). "Nudivirus genomics and phylogeny," in Viral Genomes-Molecular Structure, Diversity, Gene Expression Mechanisms and Host-Virus Interactions, ed. M. Garcia (Rijeka: InTech)
Wang, Z., Gerstein, M., and Snyder, M. (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63. doi: 10.1038/nrg2484
Webster, C. L., Longdon, B., Lewis, S. H., and Obbard, D. J. (2016). Twenty-five new viruses associated with the Drosophilidae (Diptera). Evol. Bioinform. Online 12(Suppl. 2), 13-25. doi: 10.4137/EBO.S39454
Webster, C. L., Waldron, F. M., Robertson, S., Crowson, D., Ferrari, G., Quintana, J. F., et al. (2015). The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster. PLOS Biol. 13:e1002210. doi: 10.1371/journal.pbio.1002210
Whitacre, L. K., Tizioto, P. C., Kim, J., Sonstegard, T. S., Schroeder, S. G., Alexander, L. J., et al. (2015). What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual. BMC Genomics 16:1114. doi: 10.1186/s12864-015-2313-7
Wickham, H. (2009). ggplot2: Elegant Graphics for Data Analysis. New York, NY: Springer-Verlag
Woodard, S. H., Fischman, B. J., Venkat, A., Hudson, M. E., Varala, K., Cameron, S. A., et al. (2011). Genes involved in convergent evolution of eusociality in bees. Proc. Natl. Acad. Sci. U.S.A. 108, 7472-7477. doi: 10.1073/pnas.1103457108
Wu, Q., Luo, Y., Lu, R., Lau, N., Lai, E. C., Li, W. X., et al. (2010). Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc. Natl. Acad. Sci. U.S.A. 107, 1606-1611. doi: 10.1073/pnas.0911353107
Xu, P., Liu, Y., Graham, R. I., Wilson, K., and Wu, K. (2014). Densovirus is a mutualistic symbiont of a global crop pest (Helicoverpa armigera) and protects against a baculovirus and Bt biopesticide. PLOS Pathog. 10:e1004490. doi: 10.1371/journal.ppat.1004490
Yin, X. W., Iovinella, I., Marangoni, R., Cattonaro, F., Flamini, G., Sagona, S., et al. (2013). Odorant-binding proteins and olfactory coding in the solitary bee Osmia cornuta. Cell. Mol. Life Sci. 70, 3029-3039. doi: 10.1007/s00018-013-1308-2
Yurchenko, V., Votypka, J., Tesarova, M., Klepetkova, H., Kraeva, N., Jirku, M., et al. (2014). Ultrastructure and molecular phylogeny of four new species of monoxenous trypanosomatids from flies (Diptera: Brachycera) with redefinition of the genus Wallaceina. Folia Parasitol. 61, 97-112
Zhai, Y., Attoui, H., Mohd Jaafar, F., Wang, H. Q., Cao, Y. X., Fan, S. P., et al. (2010). Isolation and full-length sequence analysis of Armigeres subalbatus totivirus, the first totivirus isolate from mosquitoes representing a proposed novel genus (Artivirus) of the family Totiviridae. J. Gen. Virol. 91(Pt 11), 2836-2845. doi: 10.1099/vir.0.024794-0