Hidden Microbiota Inhabiting in Pollen Reserves of Honey Bee ( Apis mellifera ) From Amazonas Region Revealed by DNA Metabarcoding

Pollen functions as a dynamic microbial habitat and the microbes living in pollen reserves play vital roles in pollinator health and nutrition. However, the microbiota composition of honeybee pollen reserves in biodiverse Neotropical regions remains largely unknown. This study provides the first comprehensive analysis of bacterial and fungal communities in honeybee pollen reserves across six ecosystems in the Amazonas region of Peru using high-throughput metabarcoding of the 16S rRNA gene and ITS2 markers. We found that ecosystem type is a primary driver of community structure, with bacteria and fungi responding differently to environmental changes. Despite high taxonomic heterogeneity and a limited number of shared core microbes, the main functions of these microbes were maintained, featuring enrichment of bacterial pathways involved in nutrient metabolism and saprotrophic fungal guilds. Lactobacillus and an unclassified Tremellomycetes fungus were dominant, yet their abundance varied with respect to floral resource diversity. The simplified Palm Swamp ecosystem showed significantly reduced microbial diversity, underscoring the vulnerability of these communities to habitat homogenization. Our results demonstrate that the pollen reserve microbiome is assembled through environmental filtering and pollinator-mediated selection, resulting in taxonomically flexible but functionally stable communities essential for hive processes. This work provides a foundation for understanding the microbial ecology of pollen in the Amazonas region.