Pollen diet, more than geographic distance, shapes provision microbiome composition in two species of cavity-nesting bees

Abstract

The microbial composition of stored food can influence its stability and the microbial species consumed by the organism feeding on it. Many bee species store nectar and pollen in provisions constructed to feed developing offspring. Yet, whether microbial composition is determined by the pollen types within provisions, variation between bee species at the same nesting sites, or geographic distance was unclear. Here, we sampled two species of cooccurring cavity nesting bees in the genus Osmia at 13 sites in California and examined the composition of pollen, fungi, and bacteria in provisions. Pollen composition explained 15% of variation in bacterial composition and ∼30% of variation in fungal composition, whereas spatial distance among sites explained minimal additional variation. Symbiotic microbe genera Ascosphaera, Sodalis, and Wolbachia showed contrasting patterns of association with pollen composition, suggesting distinct acquisition and transmission routes for each. Comparing provisions from both bee species comprised of the same pollens points to environmental acquisition rather than bee species as a key factor shaping the early stages of the bee microbiome in Osmia. The patterns we observed also contrast with Apilactobacillus-dominated provision microbiome in other solitary bee species, suggesting variable mechanisms of microbial assembly in stored food among bee species.

Keywords: Osmia; food microbiome; host–microbe interactions; intraspecific variation; solitary bee.

Figure 1.

Osmia bee nest structure. Osmia lignaria brood cells (A) and O. ribifloris brood cells (B) are shown in grooved wooden boards. Linear nests of each species (C) typically contain between 6 and 10 brood cells separated by partitions, each with an individual egg. Osmia lignaria constructs partitions using mud while O. ribifloris uses masticated leaf material. At each site and for each species, a maximum of three nests were sampled, with two brood cells sampled per nest. (D) Adult O. lignaria foraging on Phacelia flower. Photos by N. Williams and R. Vannette.

Figure 2.

Map of bee sampling locations (A) and variation in provision composition among sites using nonmetric multidimensional scaling. Plots of (B) pollen composition (based on Jaccard dissimilarity), (C) fungal (ITS) community composition, and (D) bacterial (16S) composition based on amplicon sequencing, visualized among bee species O. lignaria (L) and O. ribifloris (R) and sites. Ordinations were performed on a dataset including both species together but are faceted by species for clarity. Provision samples are colored by sampling site. Both species could be sampled at four sites, while O. lignaria were sampled at an additional six sites and O. ribifloris were present at an additional three sites (Table S1).

Figure 3.

Composition of (A) pollen (rbcL), (B) fungi (ITS), and (C) bacteria (16S) detected in O. ribifloris (R) and O. lignaria (L) provisions using amplicon sequencing. Relative abundance is visualized as the proportion of reads in a sample that were annotated to the focal genus with top 20 visualized, in some cases multiple ASVs within a given genus were most abundant and are collapsed for readability. The top heading in each panel indicates sampling site and within each, individual bars indicate single provisions from each bee species sampled at a given site. Because pollen composition is often not proportional to the input pollen composition due to differential extraction or amplification, we used presence/absence of a genus in all community (Jaccard) and diversity analyses. Sample sizes are in some cases unequal across amplicon datasets due to sequencing failure for a given gene region. Abbreviations for some sites were shortened, here C indicates “Clear;” A for “FR_A;” and B for Stockton-Bix.

Figure 4.

Proportion of bee provisions with Ascosphaera detection at 1% relative abundance or greater (depicted in black) in O. lignaria (L) and O. ribifloris (R) across geographic sampling locations. The absence of a bar at a given site indicates that the bee species was not available to be sampled at that site. The number of brood cells varied among sites, see Table S1 (FR sites had lower sample numbers). Bar outline colors match those in the map depicted in Fig. 2(A) above.