Mapping the eco-holobiont: tripartite interactions of small carpenter bee, floral, and soil microbiomes across an urbanization gradient

Interactions between plants and pollinating insects are essential to the health of many ecosystems, and are also of concern to human agriculture. Work in recent years has increasingly approached pollinator health from a holobiont perspective, considering communities of microbes alongside their hosts. Yet, little research has directly compared microbiomes between these insects and the environmental substrates from which they are largely acquired. We investigated the microbiome composition and structure of small carpenter bees (Ceratina calcarata) alongside directly associated samples of host flowers and soil. This study represents the first tripartite analysis of microbiomes across all three of these strata, shedding new light on the acquisition and maintenance of microbial associates in a wild pollinator species. Overall, we found that nearly all of the most common bacterial and fungal taxa detected in C. calcarata samples were shared across four species of host flowers, while soil samples showed less overlap with either flowers or bees. However, C. calcarata microbiomes still differed significantly from those of their host plants in both alpha and beta diversity, indicating that other factors are important in shaping the microbiome beyond the initial acquisition of taxa. Analysis of bees collected across a land use gradient revealed opposing patterns of association with urbanization for bacteria and fungi respectively. Conversely, variance in microbial communities for flower samples was associated more strongly with seasonality, while soil samples showed little impact of any environmental factors. Ultimately, our results support the role of flowers as a major source by which solitary bees initially acquire microbial associates, some of which are likely filtered from the soil environment. However, compositional differences in the microbiomes of C. calcarata suggest that the structure of these communities is further influenced by additional environmental factors beyond acquisition.