Investigating the viral ecology of global bee communities with high-throughput metagenomics

David A. Galbraith, Zachary L. Fuller, Allyson M. Ray, Axel Brockmann, Maryann Frazier, Mary W. Gikungu, J. Francisco Iturralde Martinez, Karen M. Kapheim, Jeffrey T. Kerby, Sarah D. Kocher, Oleksiy Losyev, Elliud Muli, Harland Martin Patch, Cristina Rosa, Joyce Megumi Sakamoto, Scott Stanley, Anthony D. Vaudo, Christina M. Grozinger

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 4 continents and Oceania. We developed a novel pipeline to rapidly and inexpensively screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences for (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 27 represented by >0.1% of the reads in a given sample, and 7 contained an RdRp or replicase sequence which could be used for robust phylogenetic analysis. This study provides a sequence-independent pipeline for viral metagenomics analysis, and greatly expands our understanding of the diversity of viruses found in bee communities.

Original languageEnglish (US)
Article number8879
JournalScientific reports
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2018

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Metagenomics
Bees
Ecology
Viruses
Oceania
DNA Viruses
RNA Viruses
Population

All Science Journal Classification (ASJC) codes

  • General

Cite this

Galbraith, David A. ; Fuller, Zachary L. ; Ray, Allyson M. ; Brockmann, Axel ; Frazier, Maryann ; Gikungu, Mary W. ; Martinez, J. Francisco Iturralde ; Kapheim, Karen M. ; Kerby, Jeffrey T. ; Kocher, Sarah D. ; Losyev, Oleksiy ; Muli, Elliud ; Patch, Harland Martin ; Rosa, Cristina ; Sakamoto, Joyce Megumi ; Stanley, Scott ; Vaudo, Anthony D. ; Grozinger, Christina M. / Investigating the viral ecology of global bee communities with high-throughput metagenomics. In: Scientific reports. 2018 ; Vol. 8, No. 1.
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abstract = "Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 4 continents and Oceania. We developed a novel pipeline to rapidly and inexpensively screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences for (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 27 represented by >0.1{\%} of the reads in a given sample, and 7 contained an RdRp or replicase sequence which could be used for robust phylogenetic analysis. This study provides a sequence-independent pipeline for viral metagenomics analysis, and greatly expands our understanding of the diversity of viruses found in bee communities.",
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Galbraith, DA, Fuller, ZL, Ray, AM, Brockmann, A, Frazier, M, Gikungu, MW, Martinez, JFI, Kapheim, KM, Kerby, JT, Kocher, SD, Losyev, O, Muli, E, Patch, HM, Rosa, C, Sakamoto, JM, Stanley, S, Vaudo, AD & Grozinger, CM 2018, 'Investigating the viral ecology of global bee communities with high-throughput metagenomics' Scientific reports, vol. 8, no. 1, 8879. https://doi.org/10.1038/s41598-018-27164-z

Investigating the viral ecology of global bee communities with high-throughput metagenomics. / Galbraith, David A.; Fuller, Zachary L.; Ray, Allyson M.; Brockmann, Axel; Frazier, Maryann; Gikungu, Mary W.; Martinez, J. Francisco Iturralde; Kapheim, Karen M.; Kerby, Jeffrey T.; Kocher, Sarah D.; Losyev, Oleksiy; Muli, Elliud; Patch, Harland Martin; Rosa, Cristina; Sakamoto, Joyce Megumi; Stanley, Scott; Vaudo, Anthony D.; Grozinger, Christina M.

In: Scientific reports, Vol. 8, No. 1, 8879, 01.12.2018.

Research output: Contribution to journalArticle

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AU - Galbraith, David A.

AU - Fuller, Zachary L.

AU - Ray, Allyson M.

AU - Brockmann, Axel

AU - Frazier, Maryann

AU - Gikungu, Mary W.

AU - Martinez, J. Francisco Iturralde

AU - Kapheim, Karen M.

AU - Kerby, Jeffrey T.

AU - Kocher, Sarah D.

AU - Losyev, Oleksiy

AU - Muli, Elliud

AU - Patch, Harland Martin

AU - Rosa, Cristina

AU - Sakamoto, Joyce Megumi

AU - Stanley, Scott

AU - Vaudo, Anthony D.

AU - Grozinger, Christina M.

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N2 - Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 4 continents and Oceania. We developed a novel pipeline to rapidly and inexpensively screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences for (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 27 represented by >0.1% of the reads in a given sample, and 7 contained an RdRp or replicase sequence which could be used for robust phylogenetic analysis. This study provides a sequence-independent pipeline for viral metagenomics analysis, and greatly expands our understanding of the diversity of viruses found in bee communities.

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Galbraith DA, Fuller ZL, Ray AM, Brockmann A, Frazier M, Gikungu MW et al. Investigating the viral ecology of global bee communities with high-throughput metagenomics. Scientific reports. 2018 Dec 1;8(1). 8879. https://doi.org/10.1038/s41598-018-27164-z