Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations

Abstract Virus symbionts are important mediators of ecosystem function, yet we know little of their diversity and ecology in natural populations. The alarming decline of pollinating insects in many regions of the globe, especially the European honey bee, Apis mellifera, has been driven in part by worldwide transmission of virus pathogens. Previous work has examined the transmission of known honey bee virus pathogens to wild bee populations, but only a handful of studies have investigated the native viromes associated with wild bees, limiting epidemiological predictors associated with viral pathogenesis. Further, variation among different bee species might have important consequences in the acquisition and maintenance of bee-associated virome diversity. We utilized comparative metatranscriptomics to develop a baseline description of the RNA viromes associated with wild bee pollinators and to document viral diversity, community composition, and structure. Our sampling includes five wild-caught, native bee species that vary in social behavior as well as managed honey bees. We describe 26 putatively new RNA virus species based on RNA-dependent RNA polymerase phylogeny and show that each sampled bee species was associated with a specific virus community composition, even among sympatric populations of distinct host species. From 17 samples of a single host species, we recovered a single virus species despite over 600 km of distance between host populations and found strong evidence for isolation by distance in associated viral populations. Our work adds to the small number of studies examining viral prevalence and community composition in wild bees.


Figure 1 :
Figure 1: Alpha diversity metrics (Shannon index, Simpson index, and Richness) describing differences in viral species diversity associated with social and solitary bees.

Figure 2 :Figure 3 :
Figure 2: Alpha diversity metrics (Shannon index, Simpson index, and Richness) describing differences in viral family diversity associated with social and solitary bees.Letters correspond to groupings by Tukey's Honest Significant Difference Test

Figure 4 :
Figure 4: Alpha diversity metrics (Shannon index, Simpson index, and Richness) describing differences in viral family diversity associated with different bee species.Letters correspond to groupings by Tukey's Honest Significant Difference Test.

Figure 5 :
Figure 5: Absolute abundance of normalized RdRP virus transcripts across sampled halictid bees in this study.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents absolute number of virus reads assigned to each family.Colors within each bar represent reads assigned to a given virus family.

Figure 6 :
Figure 6: A matrix of pairwise F st comparisons representing patterns of genetic differentiation among 17 individual populations of Narnaviridae viromes.Color represents the degree of genetic differentiation between any pair of combinations.Darker color indicates higher values of differentiation.Genetic differentiation is defined by a scale on the right side of the figure.

Figure 7 :
Figure 7: RdRP phylogeny of Phenuiviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.

Figure 8 :
Figure 8: RdRP phylogeny of Negeviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.

Figure 9 :
Figure 9: RdRP phylogeny of Reoviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.

Figure 10 :
Figure 10: RdRP phylogeny of Nodaviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.

Figure 11 :
Figure 11: RdRP phylogeny of Solemoviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.

Figure 12 :
Figure 12: RdRP phylogeny of Rhabdoviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.8

Figure 13 :
Figure 13: RdRP phylogeny of Partitiviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.

Figure 14 :
Figure 14: RdRP phylogeny of Flaviviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.

Figure 15 :
Figure 15: RdRP phylogeny of Dicistroviridae viruses.Tree is midpoint rooted for clarity only.Viruses sampled in this study are detailed highlighted in blue.Bootstrap values for select nodes are provided.Bee icon color represent species host that viral group was associated with; number represent the number of bee samples associated with viral group.The scale bar represents the number of amino acid substitutions.

Figure 16 :
Figure 16: Absolute abundance of normalized RdRP virus transcripts across sampled L. leucozonium bee hosts in this study.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents absolute number of virus reads assigned to each family.Colors within each bar represent reads assigned to a given virus family.A black dotted line indicates the average normalized viral transcript across all halictid bees sampled in this study.

Figure 17 :
Figure 17: Relative abundance of normalized RdRP virus transcripts across sampled A. mellifera.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents the relative abundance of reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 18 :
Figure 18: Absolute abundance of normalized RdRP virus transcripts across sampled A. mellifera.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents absolute number of virus reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 19 :
Figure 19: Relative abundance of normalized RdRP virus transcripts across sampled A. aurata.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents the relative abundance of reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 20 :
Figure 20: Absolute abundance of normalized RdRP virus transcripts across sampled A. aurata.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents absolute number of virus reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 21 :
Figure 21: Relative abundance of normalized RdRP virus transcripts across sampled A. pura.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents the relative abundance of reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 22 :
Figure 22: Absolute abundance of normalized RdRP virus transcripts across sampled A. pura.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents absolute number of virus reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 23 :
Figure 23: Relative abundance of normalized RdRP virus transcripts across sampled A. virescens.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents the relative abundance of reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 24 :
Figure 24: Absolute abundance of normalized RdRP virus transcripts across sampled A. virescens.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents absolute number of virus reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 25 :
Figure 25: Relative abundance of normalized RdRP virus transcripts across sampled L. versatum.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents the relative abundance of reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 26 :
Figure 26: Absolute abundance of normalized RdRP virus transcripts across sampled L. versatum.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents absolute number of virus reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 27 :
Figure 27: Relative abundance of normalized RdRP virus transcripts across sampled L. leucozonium.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents the relative abundance of reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.

Figure 28 :
Figure 28: Absolute abundance of normalized RdRP virus transcripts across sampled L. leucozonium.Each bar plot along the X-axis represents an individual sampled bee and the Y-axis represents absolute number of virus reads assigned to each species.Colors within each bar represent reads assigned to a given virus species.