Bee-microbe Interactions

We are exploring the diversity of microbes associated with solitary bee brood cells through high-throughput metagenomics in order to more fully characterize the diversity and potential roles of these microbial associates.

Bees and angiosperms are one of Earth’s most successful evolutionary and ecological partnerships. Bees gather, transport, and store floral products including pollen, nectar, and floral oils and, in the process, serve an essential role in plant reproduction: pollination. However, this bipartite relationship may involve a third hidden partner — microbes (primarily yeasts). Historical literature, more recent microbial metagenomic studies, and our own preliminary data suggest that bees rely heavily on microbes obtained from flowers for larval nutrition. The pollen/nectar provisions stored by solitary bees for larval development host a diverse microbial community rich in fermentative yeasts. Stable isotope analyses indicate that bees derive proteins and lipids from these microbial sources, meaning bees are omnivores not strict herbivores. Our project has the potential to transform the way we view the evolutionary and ecological relationships among bees, flowers, and microbes which could fundamentally rewrite the way we view pollination ecology.

Current Projects

(1) Documenting the taxonomic and functional diversity of microbes associated with 16 focal bee species spanning six of the seven families and diverse life histories. We will use both metabarcoding and culture-based methods to characterize microbial communities in bee pollen provisions to determine what biotic and abiotic factors drive bee-flower-microbe associations.

(2) Determining the degree to which our focal bee species are nutritionally dependent on microbe-derived proteins and lipids using trophic biomarkers. We will use compound-specific isotopic analysis and neutral lipid fatty acids to characterize bee dependence on microbial sources.

(3) Experimentally manipulating the microbial community of pollen provisions from two Osmia species to understand how perturbations in the microbial communities impact larval bee development. Mechanistic experiments will examine how fungal or bacterial communities influence provision quality, probe how microbial communities change as provisions age, and test mechanisms underlying microbial effects on provisions using competition assays and reverse genetic approaches.

Our research team includes collaborators from the University of Wisconsin, Madison (Shawn Steffan), the University of California, Davis (Rachel Vannette), and the University of California, Riverside (Quinn McFrederick).


Squash was first domesticated in Mexico and is now found throughout North America (NA) along with Peponapis pruinosa, a pollen specialist bee species of the squash genus Cucurbita. The origin and spread of squash cultivation is well-studied archaeologically and phylogenetically; however, no study has documented how cultivation of this or any other crop has influenced species in mutualistic interactions. We used molecular markers to reconstruct the demographic range expansion and colonization routes of P. pruinosa from its native range into temperate NA. Populations east of the Rocky Mountains expanded from the wild host plant’s range in Mexico and were established by a series of founder events. Eastern North Americawas most likely colonized from squash bee populations in the present-day continental Midwest USA and not from routes that followed the Gulf and Atlantic coasts from Mexico. Populations of P. pruinosa west of the Rockies spread north from the warm deserts much more recently, showing two genetically differentiated populations with no admixture: one in California and the other one in eastern Great Basin. These bees have repeatedly endured severe bottlenecks as they colonized NA, following human spread of their Cucurbita pollen hosts during the Holocene.

From Lopez-Uribe et al. 2016