Nationwide citizen science reveals core and rare osmotolerant yeast communities in Swedish honey

Abstract

Honey represents an extreme microbial habitat, comprising >80% sugar, low pH, oxidative stress, and antimicrobial compounds. Despite these conditions, specialized yeast species persist in nectar and honey microbial communities, where their metabolic activity may contribute to honey maturation and chemistry. To characterize the diversity and functional traits of honey-associated yeasts, we conducted a nationwide citizen science survey with the help of Swedish beekeepers, yielding ~2,400 isolates from 119 honey samples across 103 locations. Sequencing of ITS and LSU barcode regions of cultured isolates identified 85 species across 26 genera, dominated by Entelexis, Starmerella, Zygosaccharomyces, Rhodotorula, Aureobasidium, and Metschnikowia. While a small number of core taxa were consistently detected across geographic and environmental gradients, most species were rare and locally restricted, indicating a highly uneven community structure. Phenotypic assays of representative strains, typically one per isolated species, revealed broad osmotolerance, with several Entelexis, Starmerella and Zygosaccharomyces strains capable of growth at up to 80% glucose. Sugar utilization experiments showed widespread fructophilic metabolism, particularly under high-sugar conditions, and this trait was enriched among the most frequently recovered taxa. Selected isolates also fermented diluted honey, altering both its volatile profile and chemical composition. Together, these results demonstrate that honey hosts a taxonomically diverse but functionally specialized yeast community shaped by strong osmotic selection. This study establishes the largest culture-based collection of honey-associated yeasts to date, underscores the value of citizen science for large-scale microbial ecology, and identifies honey as an important reservoir of osmotolerant and fructophilic yeasts with ecological and biotechnological relevance.