Format

Send to

Choose Destination
Sci Rep. 2018 Jun 11;8(1):8879. doi: 10.1038/s41598-018-27164-z.

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

Author information

1
Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA. dag5031@gmail.com.
2
Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA.
3
Department of Biology, Pennsylvania State University, University Park, PA, USA.
4
Department of Biological Sciences, Columbia University, New York, NY, USA.
5
National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
6
Department of Zoology, National Museums of Kenya, Nairobi, Kenya.
7
Department of Plant Pathology, Pennsylvania State University, University Park, PA, USA.
8
Department of Biology, Utah State University, Logan, UT, USA.
9
Smithsonian Tropical Research Institute, Panama City, Panama.
10
Neukom Institute for Computational Science, Dartmouth College, Hanover, NH, USA.
11
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
12
Department of Beekeeping, The National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine.
13
The International Center of Insect Physiology and Ecology, Nairobi, Kenya.
14
Division of Pediatric Hematology and Oncology, Pennsylvania State University Children's Hospital, Hershey, PA, USA.

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.

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center