Bee Alert: The Microscopic and Macroscopic Perils for Bees

Aug. 7, 2020

It’s no secret: the bees are in trouble.

Biologists, beekeepers, gardeners and the general eating public have been sounding the alarm for over a decade now about the struggle of the European (or western) honeybee (Apis mellifera L.), and the precipitous decline of other native species in the Americas and Europe — as high as 50% of species in some regions. Yet research has illuminated that rather than any one predominant threat to bees, they are being accosted by multiple stressors that are synergistic in nature.

Bees are complex creatures with stunningly intricate neural networks that allow for their social structure, foraging behavior and ability to find and communicate quality food sources. While the European honeybee is widely kept in managed beekeeping hives and used to assist commercial agriculture, there are nearly 20,000 species of bees globally that act as crucial pollinators of the world’s plants. Pollinators, and especially bees, fertilize a staggering 87.5% of flowering plants worldwide, including the majority of fruit and vegetable crop species. They help ensure global food security and improve the nutritional quality of our food supply, which is even more critical as we contemplate feeding a human population projected to approach 10 billion people by 2050. In short, we need them.

But despite the mass interest and earnest research into the plight of the bees, American managed hives still saw their second highest annual loss on record between April 2019 and April 2020: 43.7%. Wild bees have also suffered significant and alarming losses.

So how did we get here?

Loss of Habitat from Aggressive Agriculture

Bees have been in decline in the United States since the 1940s. The birth of chemical fertilizers following World War II and the newly dawned age of industrial agriculture eventually transitioned many local botanically diverse family farms into large industrial monocultures. Rather than biodynamic farming and pollinator-friendly cover crops to help recover soils, industrial farms depend on chemical fertilizers and the use of pesticides and herbicides to maximize yields. These shifts have had precipitous impacts on bees, whose once-symbiotic relationship to human farming is now under threat.

Professor Marla Spivak made the astute comparison in her 2013 TEDTalk between large-scale monoculture and a pollination food desert. Enormous swaths of land used to plant single crops not only destroys native bee habitat, but sequesters acres of land where bees are unable to locate meaningful nutrition, save for the brief flowering season of a single plant species. The result is "feast or famine” for bees. This is non-trivial, as nutrient deprivation can increase bees' susceptibility to disease. It is especially damaging for native bee species, which may be most adapted to local flowering plants. Diversified farming and incorporation of wild habitat can help reduce these effects and boost bee health.

Ubiquitous Use of Pesticides, Herbicides and Other Chemicals

In focusing on lethality from acute exposure to a single chemical, many regulatory studies overlook the realistic exposure of multiple, potentially synergistic chemicals on a variety of bee outcomes, such as feeding or foraging behavior, immunity and protection from parasitic or viral disease. Pollen carried back to bee hives and honey or wax derived from it have been found laced with pesticides, herbicides, fungicides and even unclassified chemicals that may be degradation products of active ingredients.

Neonicotinoids in particular are a class of insecticide that act on the neural synapse of many insects, such as beetles or leaf hoppers. Their use sharply increased in the United States between 2003-2011. Bees are not a target organism. While some studies do not demonstrate an overtly negative effect on bees, others argue that they disrupt development of bee brain structures, suppress bee immunity, reduce feeding behavior, impair navigational ability and negatively impact social behaviors. The specific effect of neonicotinoids to weaken the immune system of queen bees may also have broad impacts for overall hive survival.

Glyphosate, the most widely used herbicide in the world, may also be impacting bees via their microbiome. Bees have 5 highly conserved core gut bacteria and several other groups that are often, but not always, present. One of the primary gut microbes, Snodgrassella alvi, is particularly important in mediating the oxidative balance of the bee gut, and also happens to be one of the species most impacted by glyphosate exposure in a dose-dependent manner. The oxygen gradient within the gut is important for anaerobic species of bacteria, meaning the loss of S. alvi, an oxygen consumer, may affect the gut community as a whole. Indeed, glyphosate exposure was also associated with a loss of Bifidobacterium spp. and predicted loss of Gilliamellia apicola, which are a core microbiome components that metabolize the complex and even toxic polysaccharides found in the bee diet. Thus the impact of glyphosate on the bee microbiome may render bees more vulnerable to opportunistic infection, nutritional deficits and increased mortality. Glyphosate has also been implicated in changes to bee development during the larval stage, including at the transcriptional level.


Possibly one of the most destructive blights to western honeybees has been parasitism and viral disease, in many cases from non-native species and emergent pathogens. Topping the list is the Varroa mite (Varroa spp.), an ectoparasite which clings to its host and feeds on the bee ‘fat body’ or metabolic center. Varroa mites are a native parasite to the Asian honeybee, Apis cerana, which has evolved a behavioral grooming mechanism to minimize their damage. They began moving westward with bee colony trade in the late 1940s, and arrived in the United States in 1987. Western honeybees do not display the same protective mechanisms as Asian honeybees, making Varroa a formidable and potentially lethal foe for a hive. If that weren’t enough, mites are also ready vectors for viruses, such as acute bee paralysis virus (ABPV) or Deformed Wing Virus (DWV), which renders bees unable to fly.

A Varroa mite clings to the back of a honeybee to feed off its fat (left); Varroa destructor, a deadly threat to Western honey bees (right).
A Varroa mite clings to the back of a honeybee, feeding on the bee fat body (left). Varroa destructor, one of the deadliest threats to Western honey bees (right).
Source: freestockphoto (left) and (right)

Bees are afflicted by numerous other blights from across the phylogenetic tree of life. The hive beetle Aethina tumida is another foe to western honeybees, introduced within the last several decades, that damages the hive and consumes the bee young. Microsporidians of the Nosema genus (1 species of which was also recently introduced to western honeybees) are gut parasites that change the honeybee microbiome and alter metabolic pathways in the bee. Many viruses also parasitize bees, the foremost of which is sacbrood virus (SBV), which predominantly attacks larval tissues and impairs healthy hive growth.

The most recent introduction of the so-called “murder hornets” (Asian giant hornet, Vespa mandarinia) to the United States and Canada in late 2019 is yet another alarming development for western honeybees. The Asian honeybee, which co-evolved with V. mandarinia, has developed a defense mechanism in which a scout hornet entering a hive is smothered by an ambush of hundreds of bees, who beat their wings and raise the temperature and carbon dioxide level. This ‘bee ball’ heats and suffocates the hornet to death, staving off future attack. European honeybees, by contrast, have not developed adequate defense against the hornet, leaving them vulnerable to the rapid massacre of an entire hive in a single attack. V. mandarinia has so far only been sighted in regions of Canada and northern Washington state, and active efforts are underway to eliminate its existence in the Americas.

Climate Change

Climate change is famously responsible for the destruction and movement of habitats and its threat to biodiversity. However, for bees in particular, rising carbon dioxide levels directly affect the protein content of one of their primary food sources: pollen. Bees derive their entire foraging diet from nectar (carbohydrates) and pollen (protein), and may have limited sources of pollen during late season gathering. Nutritional deficits in pollen specifically reduce the bee’s ability to ward off invading pathogens, and can have long-term effects on the growth of a colony.

Beekeeping Practices

In nature, species adapt to selective pressures that generally favor those most able to overcome the stressors at hand. This applies to parasites too, which must strike the right balance between host immunity and disease spread to be successful. Highly virulent pathogens run the risk of killing off their host reservoir and being unable to spread, thus the selective pressure for many pathogens is to reduce virulence over time or elect tradeoffs with the host.

However, modern beekeeping practices can artificially remove the stressors that promote such evolutionary calibration and instead provide an environment that inadvertently selects for greater disease spread and more virulent pests. This happens in the following ways:

  • Increased Population Density: While wild beehives house approximately 18,000 bees, commercial bee colonies can range from 20,000 to 52,000. This increased density makes bees more vulnerable to disease. Moreover, larger commercial apiaries are likely to cluster colonies together, which is associated with higher mite load and reduced colony survival. Clustered hives have higher rates of drifting (bees that enter a different hive), which increases pathogen spread.
  • Artificial Repopulation: When a hive is devastated by a disease, the pathogen’s ability to spread is limited because there are no new hosts to infect. However, in managed hives, an entirely new colony of susceptible individuals is brought in to replace the dying hive. This removes the selective pressure for a pathogen to reduce virulence, and instead rewards the most deadly pathogens. However, building colonies from survivors can help strengthen the bees.
  • Incomplete Pest Removal: Treatments that only partially reduce pathogen volume without destroying them, such as routine application of miticides for Varroa spp., select for resistance and more hardy pathogens.
  • Agricultural Travel: Many managed honeybees follow a national circuit according to agricultural pollination needs. It’s estimated that over half of all managed honeybee colonies in the United States migrate to California to help pollinate during almond season. What this means practically is that bees from all over the nation are congregated in one setting, which presents the risk of disease spread across multiple geographical locations when the bees return home. There have also been reports of toxic pesticide exposures from such travel.

Colony Collapse and the Synergistic Effects of Multiple Stressors

Although each of these stressors are formidable on their own, the real threat is in their synergy.

For example, pesticides and herbicides are thought to be sublethal for bees. However, the demonstrated effect on bee immunity contributes to exposed bees' susceptibility to pathogens. Meanwhile, bees are facing a higher pathogenic risk due to a combination of non-native parasites for which they don’t have an evolved defense, and commercial practices that put them at greater risk of disease spread. The added effect of chemicals, such as glyphosate, on the bee microbiome reduces their natural defenses even more, along with their nutritional status. Moreover, alterations to bee navigational capacity from neonicotinoids interfere with the foraging behavior of bees, making it difficult to bolster immunity with good nutrition. On top of that, climate-induced changes to plant chemistry reduce the nutritional benefit of each foraging venture. The compounding malnourishment of the bees makes them susceptible to further disease in an unvirtuous cycle.

A particular form of hive failure known as colony collapse disorder (CCD) occurs when the majority of adult bees in the hive disappear, leaving only a queen, some nurse bees with larvae and plenty of food stores. Dead bee bodies are nowhere to be found. No single factor has been shown to definitively cause CCD, and it likely arises from a constellation of stressors. However, pathogenic assault on a hive is often a factor and several bee pathogens are associated with it.

It’s not just the honeybees. Wild bees are exposed to many of the same chemicals and environmental stressors that managed colonies are, with the added impact of habitat loss. Where foraging habitats are shared between managed and native bees, diseases fostered in a managed environment can also jump to wild hives and impact their survival as well.

How You Can Help the Bees

Despite the many stresses facing bees, each of us can do something to help. The following are simple ways to boost bees in your area:

  • Plant Bee-Friendly Flowers: This is possibly the simplest and most delightful way to help your neighborhood bees. Whether it’s a single little pot of flowers outside your door or a large vegetable garden, flowering plants provide vital sources of the 2 main bee foods: nectar and pollen.
  • Buy Organic: We tend to think of organic produce in terms of human health, but perhaps we should also think of the ecosystem that it supports. Organic crops can provide non-contaminated foraging space for bees on a large scale. Studies find that organic farms near diversified habitat retain an abundance of native bees in the area, whereas all other farms experience a much-reduced abundance and diversity of native bee species. As your budget allows, buying organic produce is a simple way to support bee-friendly agriculture.
  • Build a “Bee Hotel” to Shelter Local Bees: Many native bee species are non-aggressive and solitary. Providing them with safe habitat (think birdhouse) is a fun and educational way to help local pollinators thrive, especially in conjunction with a garden or nearby park.
  • Reconsider Pesticides on Landscaped Plants: Agriculture is not the only source of chemical exposure for bees. Landscaped and gardened plants are still a source of pesticide and herbicide exposure for local foraging bees. If you have a yard with plants or flowering trees, consider growing them without the use of chemicals.
Two-in-one image shows a bee hotel and bee-friendly flowers.
A bee hotel (left) is a simple, easy way to support native solitary (non-hive forming) bee populations. Planting bee-friendly flowers (right, lavender) is another excellent way to provide for bees in your area.
Source: (left) and (right)

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Author: Christy Clutter, Ph.D.

Christy Clutter, Ph.D.
Christy Clutter, Ph.D., is a scientist, microbiome aficionado and writer whose research work focused on gut immunity and the microbiota, along with public health disparities in nutrition.