Supplementary code and data for: Symbiotic bacteria and fungi proliferate during diapause and may enhance overwintering survival in a solitary bee

Host-microbe interactions underlie the development and fitness of many
macroorganisms, including bees. Whereas many social bees benefit from
vertically transmitted gut bacteria, current data suggests that solitary
bees, which comprise the vast majority of species diversity within bees,
lack a specialized gut microbiome. Here we examine the composition and
abundance of bacteria and fungi throughout the complete life cycle of the
ground-nesting solitary bee Anthophora bomboides standfordiana. In
contrast to expectations, immature bee stages maintain a distinct core
microbiome consisting of Actinobacterial genera (Streptomyces,
Nocardiodes) and the fungus Moniliella spathulata. Dormant (diapausing)
larval bees hosted the most abundant and distinctive bacteria and fungi,
attaining 33 and 52 times their initial copy number, respectively. We
tested two adaptive hypotheses regarding microbial functions for
diapausing bees. First, using isolated bacteria and fungi, we found that
Streptomyces from brood cells inhibited the growth of multiple pathogenic
filamentous fungi, suggesting a role in pathogen protection during
overwintering, when bees face high pathogen pressure. Second, sugar
alcohol composition changed in tandem with major changes in fungal
abundance, suggesting links with bee cold tolerance or overwintering
biology. We find that Anthophora bomboides hosts a conserved core
microbiome that may provide key fitness advantages through larval
development and diapause, which raises the question of how this microbiome
is maintained and faithfully transmitted between generations. Our results
suggest that focus on microbiomes of mature or active insect developmental
stages may overlook stage-specific symbionts and microbial fitness
contributions during host dormancy.