Comparing virome composition between honey bees (Apis mellifera) and small carpenter bees (Ceratina calcarata) in response to various agricultural landscapes

Bees are the quiet architects of our food supply and wild landscapes. Without them, many flowers would never set fruit, and the ecosystems that depend on those fruits would unravel. For decades, scientists have known that these hardworking insects face a growing threat from invisible enemies: viruses. While we have long studied the viruses that plague managed honey bees, the tiny, wild cousins that live alongside them remain a mystery. These wild bees, often solitary and less studied, might be carrying different viruses, or perhaps the same ones, moving between species as they visit the same flowers. Understanding who carries what, and how the landscape they live in changes the mix of viruses they encounter, is crucial for protecting the health of all pollinators.

A team of researchers set out to map this hidden world of bee viruses by comparing two very different species living in the same region. They focused on the familiar honey bee, a managed species kept in hives by farmers, and the small carpenter bee, a wild species native to North America that builds its nests in hollow stems. The scientists wanted to see if the type of land these bees foraged on—whether it was a conventional farm using standard pesticides, an organic farm with diverse flowers and no synthetic chemicals, or a roadside patch of greenery—shaped the viruses living inside them. To do this, they collected hundreds of foraging bees from these three distinct environments in New Hampshire. Instead of looking for a single virus, they used a powerful genetic sequencing technique to read the entire collection of viral RNA present in the bees, effectively taking a snapshot of every virus they were carrying at that moment.

The results revealed a clear divide between the two species. The honey bees carried a wide and busy assortment of viruses, including several known pathogens that can cause deformities or death in bee colonies. They also harbored a surprising number of plant viruses, likely picked up from the pollen and nectar they consumed. In contrast, the wild small carpenter bees carried far fewer viruses overall. Their viral load was lighter, and the types of viruses they carried were different. Most notably, the researchers discovered three new viruses that had never been seen before in these bees. Two of these were related to a family of viruses known to infect insects, and one appeared to be a type of poxvirus, a group usually associated with larger insects like flies or wasps. One of the new insect viruses was found in both the honey bees and the wild bees; however, in the honey bees, it was detected as a negative strand, a sign of active replication, suggesting the virus was actively infecting the honey bees rather than just being passively shared.

The landscape where the bees lived also played a role, though the effect was subtle and varied by species. In the honey bees, the common, dangerous viruses were present everywhere, regardless of whether the bees were on an organic farm, a conventional farm, or a roadside. However, some of the less common viruses, including a specific segment of a Lake Sinai virus and a Hubei partiti-like virus, were found in higher numbers on the organic farms. This suggests that the diverse flowers and lack of pesticides in organic settings might change how viruses circulate, perhaps by supporting a wider variety of viral strains or by altering the bees' immune systems. In contrast, the wild bees showed an even sharper response to their environment. Several viruses that were found on the conventional farms and roadside areas were completely absent from the bees collected on organic farms. Furthermore, levels of a specific plant virus, White clover cryptic virus 1, were significantly lower in organic farms compared to conventional farms and roadside habitats. This indicates that the wild bees are more sensitive to their surroundings, and their viral communities are tightly linked to the specific plants and conditions they encounter.

Perhaps the most striking finding was the discovery of these new viruses in the wild bees. The researchers found that the small carpenter bee hosts a unique set of viral passengers, including a potential new poxvirus that is closely related to viruses found in other insects but has never been documented in this bee species before. This discovery expands our understanding of what viruses exist in nature and highlights that wild bees are not just passive victims of honey bee diseases; they are hosts to their own distinct viral communities. The study also confirmed that while honey bees act as a reservoir for many known pathogens, the wild bees are not simply catching the same diseases in the same way. Their viral profiles are distinct, shaped by their specific biology and the unique landscapes they inhabit.

Ultimately, this research paints a picture of a complex, dynamic relationship between bees, viruses, and the land they share. It shows that the health of a pollinator is not just about the species itself, but about the specific environment it lives in and the unique mix of viruses it carries. The fact that wild bees carry different viruses, and that these viruses change depending on whether the land is managed organically or conventionally, suggests that protecting wild pollinators requires more than just saving the honey bee. It requires preserving the diverse habitats that support their unique biology. By mapping these viral communities, scientists are beginning to understand the invisible forces that shape pollinator health, offering a clearer path toward protecting the insects that feed our world.