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Abstract 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 highly 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 A. 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.
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This content will become publicly available on March 10, 2026
Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly
Abstract Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiomes have been central models for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi- kingdom interactions. Stingless bees, highly eusocial managed bees that rely on yeast for larval development, offer a valuable complementary system to study microbiome assembly, and within an eco-evolutionary framework. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of stingless bee microbiome assembly. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also actively maintained through highly selective bacterial-fungal interactions. Our findings uncover multi-layered mechanisms shaping an eusocial insect microbiome, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.
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- Award ID(s):
- 2022049
- PAR ID:
- 10629060
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Institution:
- bioRxiv
- Sponsoring Org:
- National Science Foundation
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