Data sets

Bacteria and fungi play vital roles in bee health and development, yet microbial symbionts remain largely uncharacterized for most bee species, particularly ground-nesting taxa and the food stored for their offspring. Microbial mutualists and commensals may prevent pollen provision spoilage, liberate nutrients from pollen, supply direct nutrition, and/or suppress pathogens, though these functions appear context-dependent and variable among hosts. To characterize relationships among developing bees and their microbes, we analyzed 346 ‘live’ brood cell pollen provisions representing 39 species, 18 tribes, and six bee families spanning diverse life histories (solitary, facultatively social, and weakly social), diet breadths (generalist or specialist: also, pollen- and oil-collecting), and nesting substrata (ground, stem, wood and cavity). Microbial composition was determined by amplicon sequencing of bacterial 16S rRNA (V5–V7) and fungal ITS (1 and 2) regions. Bacterial diversity was significantly influenced by bee taxonomy, phylogeny, floral resource use, and life history, while fungal diversity was primarily structured by host taxonomy, phylogeny, and nesting substrata. Across phylogenetically distant bee tribes, pollen provisions were often dominated by lactic- or acetic acid-producing bacteria, indicating a convergent strategy of microbial fermentation that reduces bacterial richness and may enhance food preservation. In contrast, fungal communities exhibited greater compositional variability and lacked consistent associations. Together, these results reveal broad evolutionary and ecological patterns underlying the microbiome of solitary bee brood cells and suggest that acid-producing bacteria play a stabilizing role in the preservation and function of pollen provisions.