Microbial Ecology

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.

Solitary, ground-nesting bees, which comprise the vast majority of bees in the world, store a mixture of nutrient-rich pollen, nectar and, sometimes, floral oils in brood cells excavated from the soil. The semi-liquid provision mass represents a rich store of resources in the form of carbohydrates (primarily from nectar), proteins (primarily from pollen), and diverse plant secondary compounds. This pollen provision mass not only sustains the larval bee, but it can also be host to a diverse microbial fauna, although the role of these microbes in this mini-ecosystem is largely unknown.

Current Projects

Current research in this area is being conducted by graduate student Kristen Brochu, and focuses on the hoary squash bee Peponapis pruinosa in New York State. This bee is an ideal study species because its nests can be easily excavated allowing pollen provisions to be collected for analysis of pesticides, and screened for the presence of pathogenic and mutualistic bacteria and fungi.

Although managed bees, such as honey bees, can be effective pollinators in many crops, colonies are costly to rent, and some high value crops, such as cucurbits (squashes and pumpkins), are actually pollinated more effectively by solitary, ground nesting bees such as P. pruinosa. Managing wild bees is therefore a more economic and efficient strategy to improve crop yield. This research will ultimately provide specific management guidelines for maintaining healthy populations of wild ground nesting bees in agroecosystems in New York State.


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