Bee Microbiomes Across Phylogeny and Functional Traits: Examining Host-Cleptoparasite Associations

Studies on microbiomes are essential for understanding the various roles microbes play in the health of bees, yet many wild bees including cleptoparasitic species and their microbiomes continue to be underexplored. To alleviate this gap, we analyzed bacterial and fungal microbiomes of cleptoparasitic species with 16 S rRNA and ITS1 metabarcoding and compared results to the microbiomes of their hosts and other wild bees across families and functional traits. We found that a parasitic lifestyle was associated with a significantly more diverse bacterial microbiome compared to other social or dietary traits, and that ground-nesting bees have a richer bacterial microbiome than stem-nesting bees. Fungal diversity was only found to be greater in solitary bees compared to eusocial species. Hosts and cleptoparasites had broadly similar bacterial and fungal microbiomes, with a few exceptions. N. articulata had a significantly more diverse bacterial microbiome compared to its hosts Agapostemon virescens and A. sericeus, and H. calliopsidis boasted greater bacterial diversity compared to its host Calliopsis andreniformis. Fungal communities were also different for N. illinoensis - Andrena crataegi and for N. articulata - A. virescens, whereas several host-cleptoparasite pairs harboured distinct bacterial communities. Individual cleptoparasites were also uniquely associated with several understudied bacterial microbes. Our study is the first to assess the microbiomes of six cleptoparasitic species and reveals important insight into the unique and shared microbes in wild bees and host-cleptoparasite pairs.