Microbial allies in bee nests

Introduction

Bee nests represent complex microbial ecosystems, shaped by the remarkable diversity of bee species and their nesting behaviours. The architectural variety – from the elaborate wax combs of honey bees to the enclosed resinous cavities of stingless bees and the soil or plant-based burrows of solitary bees – creates distinct microhabitats that support specialised microbial communities (Fig. 1). These microenvironments vary in temperature, humidity, substrate composition and chemical profiles and host diverse assemblages of bacteria, yeasts and filamentous fungi.^1,2 As bees forage, they introduce microbes from floral nectar, pollen, soil and other environmental sources into their nests, continuously shaping the microbial landscape.³ These microbial communities interact with nest materials, the bees themselves, and each other, forming a dynamic and responsive ecosystem, influenced by both environmental inputs and host-mediated factors.⁴

Fig. 1.

Diverse bee nest architecture. Clockwise from top left: managed Apis mellifera hive (photograph by Ivan Radic, CC BY 2.0), wild Apis cerana nest in China (photograph by CBCGDF, CC BY 4.0), wild Dasypoda hirtipes ground nest in Germany (photograph by Dellex, CC BY 4.0), managed Tetragonula carbonaria hive in Australia (photograph by Kenya Fernandes), wild Nannotrigona testaceicornis nest in Brazil (photograph by Carlos Raposo, CC BY 4.0), wild Xylocopa sp. wood cavity nest in the United States (photograph by Thom Wolf, CC BY 4.0).

Research on bee–microbe interactions has expanded dramatically over the past two decades, driven by advances in molecular techniques and growing recognition of microbial contributions to bee health. However, this burgeoning field has disproportionately focused on honey bees (Apis mellifera), leaving significant knowledge gaps regarding microbial dynamics in the ~20,000 other bee species worldwide. As pollinators face unprecedented threats from habitat loss, pesticide exposure and climate change, understanding these microbial relationships across diverse bee taxa has become increasingly urgent for both conservation and agricultural sustainability.

Microbial roles in bee food products

Microorganisms are integral to the production, preservation and protection of bee food products like bee bread and honey. These food sources provide essential nutrients for bee growth and development, with microbes influencing their antimicrobial activity, chemical composition and stability within the hive. The relationship between bees and their microbial communities represents an evolutionary adaptation that enhances colony nutrition and helps defend against spoilage and pathogens.

Bee bread, a protein-rich resource crucial for nutrition in social bees, undergoes significant microbial transformation from raw pollen (Fig. 2). In honey bee colonies, workers mix pollen with glandular secretions containing enzymes, peptides and proteins, along with small amounts of nectar or honey.⁵ This mixture is packed into wax cells where microbial activity, particularly from lactic acid bacteria and yeasts, facilitates fermentation.⁶ This process lowers the pH, breaks down complex nutrients and produces antimicrobial compounds that inhibit pathogen growth and prevent spoilage. Similar microbial processes with community succession have been observed in other bee taxa such as Osmia and Megachile spp.,⁷ although the specific dynamics of fermentation are less well-characterised.

Fig. 2.

From pollen to bee bread. Pollen collected from flowers by forager bees undergoes microbial fermentation, transforming it into bee bread (photos by Elizabeth Frost). Adapted from Fernandes et al.²²

Honey, primarily a carbohydrate-rich food source, also benefits from microbial stabilisation. Fresh nectar collected by forager bees is rich in sugars but highly perishable due to its high water content. Honey bees predominantly preserve nectar by physical means, reducing moisture content below ~20% through regurgitation and evaporation,⁸ although microorganisms play a role by contributing antimicrobial compounds such as peptides and organic acids that further help preserve the honey.⁹ By contrast, stingless bees (Meliponini spp.) maintain honey with a higher moisture content (~30–40%), and microbial fermentation plays a more prominent role in its preservation.¹⁰ Lactic and acetic acid bacteria, along with yeasts, lower the pH and produce antimicrobial metabolites, contributing to the distinctive pH and bioactive properties of stingless bee honey.

Microbial communities of bee bodies

The microbial ecosystem of bee nests extends beyond hive products to the bees themselves, which harbour diverse microbial communities that play essential roles in digestion, immunity and protection.¹¹ Among these, the gut microbiome is the most extensively characterised, particularly in honey bees where a core set of bacterial species has co-evolved with their hosts over millions of years.¹² This microbiome primarily comprises Gilliamella, Snodgrasella, Apilactobacillus Firm-4, Bombilactobacillus Firm-5 and Bifidobacterium. These species help break down complex plant polysaccharides and detoxify harmful secondary metabolites from floral resources,¹³ mediate immune defence pathways¹⁴ and provide vital protection against pathogens.¹¹

Other social bees, such as bumblebees (Bombus spp.) and stingless bees, share some of these core bacterial lineages with honey bees but generally exhibit greater compositional variability.^15,16 By contrast, although some solitary bees show reasonably stable associations with certain microbes, others host more transient, environmentally derived microbial communities with seemingly few host-specific symbionts.¹⁷ This difference is likely a reflection of their diverse foraging behaviours and independent nesting habits, which result in more variable microbial exposure compared to social species.

In addition to the gut, bees also harbour microbial communities on their exoskeleton, forming the cuticular microbiome. This external microbial layer serves as an additional line of defence, with many microbes producing antimicrobial compounds that help prevent pathogen colonisation.¹⁸ The finding that solitary bees host a more complex and diverse array of microbes than social bees, suggests that the cuticular microbiome is affected by visited plants, lifestyle and adaptation to temperature.¹⁹ Microbes have also been detected in honey bee drone reproductive tissue, although their possible functional roles in fecundity and health have yet to be characterised.²⁰

Environmental stressors that perturb bee microbes

As we gain understanding of how microbes support nest stability and bee health, it is becoming increasingly clear that external stressors that disrupt these microbial communities can have significant consequences. Bees face a complex array of environmental challenges that can disrupt their microbial ecosystems, alter host–microbe interactions and heighten susceptibility to diseases. Multiple interacting anthropogenic and environmental factors, including habitat loss and fragmentation, agricultural intensification, pesticide exposure and climate change, influence the composition and functionality of both hive-associated and bee-hosted microbiomes. Recent research by myself and colleagues has shown that even minor stress can have cascading effects throughout the hive ecosystem, simultaneously affecting honey antimicrobial activity, altering microbial communities in pollen products, and disrupting gut microbiome composition in resident bees.^21,22

Among these factors, pesticides pose one of the most significant and well-documented risks. Agricultural chemicals can directly alter the gut microbiome of honey bees, reducing microbial diversity and impairing essential functions related to digestion, detoxification and immune regulation.²³ Similar disruptions have been observed in bumblebees exposed to glyphosate-based herbicides, suggesting broad impacts across bee taxa.²⁴ Pathogens also play a role in disrupting bee microbiomes, with microsporidian infection caused by Nosema spp. interfering with gut microbial stability in honey bees.²⁵ These pathogens can outcompete beneficial microbes and alter the metabolic environment of the gut. Additionally, antibiotic treatments used to control bacterial diseases in managed bee colonies can unintentionally eliminate beneficial gut bacteria, reducing overall microbial resilience and increasing vulnerability to opportunistic infections.²⁶

Beyond chemical and biological threats, ecological changes significantly impact bee-associated microbes across species. Habitat loss and agricultural intensification restrict foraging options, leading to nutritional stress and likely limiting microbial acquisition from environmental sources.²⁷ Wild bees foraging in monoculture landscapes encounter reduced diversity of floral-associated microbes, which may impair nutrition, immunity and fitness, particularly in specialised solitary bee species with specific pollen requirements.³ Climate change further compounds these challenges by altering flowering patterns²⁸ and therefore microbial ecology.

Implications for beekeeping and conservation

Microbes play a crucial role in bee health, with direct implications for both beekeeping practices and pollinator conservation efforts. For beekeepers managing honey bees, understanding microbial contributions to hive health can inform practices that promote beneficial microbiomes – including minimising pesticide exposure, ensuring diverse forage access and maintaining optimal hive conditions. Recent research exploring targeted probiotic supplements to restore beneficial microbes and counteract environmental stressors in managed colonies have shown promising preliminary results with decreases in pathogen load²⁹ and increases in brood population and harvestable honey.²³ These microbiome-aware techniques may significantly improve colony survival rates and adaptive responses in the face of increasing environmental challenges.

Conservation strategies too must recognise the diverse microbial ecosystems that exist across bee taxa, from highly social honey bees and stingless bees to primitively social bumblebees and solitary bees. Habitat preservation that maintains plant diversity directly supports microbial diversity in bee food products and gut communities, strengthening overall pollinator resilience. Restoring native floral communities not only provides essential pollen and nectar but also facilitates the transmission of key microbial symbionts necessary for bee health. With wild bee populations declining worldwide³⁰ a deeper understanding of bee–microbe interactions provides new insights for conservation, highlighting the need to protect both the macroscopic and microscopic components of their ecology.