Investigating interaction between genotype and microbiome profile in Irish honeybees

Previous work from our group identified distinct microbiome profiles in thriving versus non-thriving honeybee colonies in southwest Ireland, and highlighted seasonality, rather than location, as a significant factor in microbiome dynamics. Ireland harbours a relatively pure population of Apis mellifera mellifera, a subspecies in decline across mainland Europe, that is threatened by introgression from imported honeybee types such as the Buckfast hybrid and C-lineage honeybees. In this pilot study, we identified mitotypes of 30 honeybee colonies across southern Ireland and sequenced the nuclear genome of 9 colonies to assess hybridization levels. We profiled the microbiome of these colonies to investigate if mitotype interacted with the microbiome. Of the 30 colonies tested, 18 were M-mitotypes, but 9 C- and 3 A-mitotypes were also detected. Nuclear genome SNP analysis revealed that M-mitotype colonies were relatively pure, displaying little to no introgression, whereas A-mitotypes displayed a hybridised genome predominantly composed of M-lineage SNPs. C-mitotype colonies also displayed varying levels of M-lineage SNPs. Microbiome composition did not differ significantly across mitotypes, with individual colony being the most significant determinant of microbiome diversity. These findings provide further evidence that the Irish honeybee population is predominantly composed of native M-lineage honeybees, though its genetic integrity is threatened by the presence of imported lineages. While this native population does not possess a unique microbiome compared to that of other lineages, these results further our understanding of factors which determine the microbiome composition of honeybee colonies in Ireland.