Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria

RRH: Environmental Drivers of Bee Microbiome


Wild bees encounter environmental microbes while foraging. While environmental context affects bee diversity, little is known about it how affects the wild bee microbiome. We used field surveys in 17 urban gardens to examine whether and how variation in local and landscape habitat features shapes the microbiome of the solitary Blue Orchard Bee, Osmia lignaria. We installed O. lignaria cocoons at each site, allowed bees to emerge and forage, then collected them. We measured local features of gardens using vegetation transects and landscape features with GIS. We found that in microbiome composition between bee individuals varied by environmental features such as natural habitat, floral resources, and bee species richness. We also found that environmental features were associated with the abundance of bacterial groups important for bee health, such as Lactobacillus. Our study highlights complex interactions between environment context, bee species diversity, and the bee-associated microbes.

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Data Accessibility

We have uploaded our code, data, and metadata to a dryad repository at https://doi.org/10.6086/D1H094. We added sequencing data to SRA, accession #PRJNA613243.


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S. Solstice-Thomas, M. Plascencia, M. Otoshi, R. Quistberg, and S. Albuquerque surveyed wild bee communities and identified specimens. P. Bichier assisted with study design and collecting vegetation data. M. Egerer assisted with vegetation data collection. P. Graystock, H. Vuong, K. Russell, and J. Rothman provided advice for laboratory and data analysis protocols. H. Eckelhoefer provided support with sequencing. The following gardens allowed us to conduct the research at their sites: Aptos Community Garden, Beach Flats Community Garden, Berryessa Community Garden, Center for Agroecology and Sustainable Food Systems, Chinatown Community Garden, Coyote Creek Community Garden, El Jardín at Emma Prusch Park, The Forge at Santa Clara University, Giving Garden at Faith Lutheran Church, Homeless Garden Project, La Colina Community Garden, Laguna Seca Community Garden, The Live Oak Grange, MEarth at Carmel Valley Middle School, Mi Jardín Verde at All Saints’ Episcopal Church, Our Green Thumb Garden at Monterey Institute for International Studies, and Salinas Community Garden at St. George’s Episcopal Church.


Funding was provided for HC by the Heller Agroecology Award and the Daniel Gaines Award from the University of California, Santa Cruz, the Centennial Pollinator Fellowship from Garden Club of America, public backers supporting a crowdfunding campaign. Funding also provided by USDA-NIFA Award 2016-67,019-25,185 to SMP.

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HC acquired funding for the research, led study design, fieldwork, lab work, and coordinated manuscript writing and publication. QSM contributed to field research design, provided physical and financial access to laboratory equipment, supervised laboratory methods, and contributed to the manuscript. SMP contributed to field research design, fieldwork logistics, data analysis, and manuscript writing.

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Correspondence to Hamutahl Cohen.

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Cohen, H., McFrederick, Q.S. & Philpott, S.M. Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria. Microb Ecol (2020). https://doi.org/10.1007/s00248-020-01549-y

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  • Microbiome
  • Bee-microbe interactions
  • Horizontal-transmission
  • Urban gardens