Changes in transcript abundance relating to colony collapse disorder in honey bees (Apis mellifera)

Abstract

Colony collapse disorder (CCD) is a mysterious disappearance of honey bees that has beset beekeepers in the United States since late 2006. Pathogens and other environmental stresses, including pesticides, have been linked to CCD, but a causal relationship has not yet been demonstrated. Because the gut acts as a primary interface between the honey bee and its environment as a site of entry for pathogens and toxins, we used whole-genome microarrays to compare gene expression between guts of bees from CCD colonies originating on both the east and west coasts of the United States and guts of bees from healthy colonies sampled before the emergence of CCD. Considerable variation in gene expression was associated with the geographical origin of bees, but a consensus list of 65 transcripts was identified as potential markers for CCD status. Overall, elevated expression of pesticide response genes was not observed. Genes involved in immune response showed no clear trend in expression pattern despite the increased prevalence of viruses and other pathogens in CCD colonies. Microarray analysis revealed unusual ribosomal RNA fragments that were conspicuously more abundant in the guts of CCD bees. The presence of these fragments may be a possible consequence of picorna-like viral infection, including deformed wing virus and Israeli acute paralysis virus, and may be related to arrested translation. Ribosomal fragment abundance and presence of multiple viruses may prove to be useful diagnostic markers for colonies afflicted with CCD.

Fig. 1.

Experimental design for microarray comparisons of CCD and healthy bees. East coast CCD includes bees collected in Florida and Pennsylvania, and west coast CCD includes bees from California. Guts from bees remaining in colonies that were classified as mild or severe were compared with each other and together, through a reference gut RNA sample, with guts of healthy historical bees collected in 2004 and 2005. A total of 22 microarrays were hybridized.

Fig. 2.

Heatmap showing expression values for 65 probes demonstrating differential expression in 3 contrasts: east coast CCD versus historical, west coast CCD versus historical, and east coast severe versus east coast mild [P < .01 (FDR); fold-change >2]. Yellow indicates increased transcript abundance and red indicates decreased transcript abundance relative to the mean for all colonies. Probes lacking a description correspond to EST sequences for which no matching gene has been found. More information about the probes is provided in Table S5. CA, California; PA, Pennsylvania; FL, Florida. Numbers correspond to colony number. S, severe CCD; M, mild CCD. Colonywise clustering was performed using expression values for all 6,777 probes. Euclidean distances were calculated and clustered using the “complete” method.

Fig. 3.

Venn diagram showing the number of transcripts up-regulated and down-regulated in 3 comparisons: west coast (California) CCD versus historical, east coast (Florida and Pennsylvania) CCD versus historical, and east coast severe CCD versus mild CCD.