In a new study, experts from York University assert that the local environment plays a crucial impact on the health and variety of the gut microbiome of wild bees, which could aid in the detection of invisible stressors and early warning signs of potential threats.

Researchers in North America, Asia, and Australia sequenced the entire genomes of three species of carpenter bees to serve as a pilot project in the emerging field of metagenomics. Through this analysis, they were able to learn more about the bee’s gut microbiome (which is made up of bacteria and fungi), diet, viral load, and environmental DNA.

Researchers found that solitary bees, unlike social bees like honeybees and bumblebees, get their microbiome, which is important for health, from the environment where they look for food instead of from their nest mates. Instead of building hives, carpenter bees dig into the woody stems of plants to lay their eggs.

“This may make them better bio-indicators as they are much more sensitive to their environment,” explains Sandra Rehan, corresponding author of the study.

In Australia, the metagenomes and microbiomes of the local populations were so different that machine learning tools could reliably tell from which population each bee came.

Crop pathogens formerly solely reported in honeybee microbiomes were also discovered in the microbiomes of carpenter bees.

“These pathogens are not necessarily harmful to bees,” adds Rehan, “but these wild bees could potentially be vectoring diseases that might have negative effects on agriculture.”

It’s crucial to figure out how these viruses spread in wild bees since bees contribute to global ecological and agricultural health, as well as providing more than $200 billion in annual agricultural services.

Establishing a baseline for what a healthy microbiome in wild bees looks like enables scientists to compare species across continents and populations, as well as to determine how diseases and harmful bacteria are being introduced and spread.

“We can really dissect bee health in a very systematic way looking at population genetics and parasite pathogen loads, healthy microbiomes and deviations,” says Rehan. “The long-term goal is really to be able to use these tools to be able to also detect early signatures of stress and habitats in need of restoration or conservation. To develop it almost like a diagnostic tool for bee health.”

For the first time, researchers believe they have caught the core microbiome of carpenter bees. Beneficial bacteria were discovered in all three carpenter bee species, which aided metabolic and genetic activities. They also discovered Lactobacillus species, which are a type of helpful bacteria that is necessary for gut health and can be found in most bee lineages. Lactobacillus has been shown to defend against common fungal diseases, strengthen the immune system, and aid nutrient absorption.

Rehan and her graduate student Phuong Nguyen recently published a paper in the journal Environmental DNA, which looked at the microbiome in brood and adult carpenter bees in cities and discovered they were lacking Lactobacillus.

““This raises red flags,” Rehan says. “We are continuing those studies to look at more nuanced urban, rural comparisons and long-term data to really understand these environmental stressors. Anytime we characterize a microbiome and see deviations from what we know to be normal, it can give us an indication of a population or species in threat.”

Overall, the findings suggest that metagenomic approaches could provide valuable information about wild bee ecology and health in the future.

“We’ve been piloting this research approach in a few species, but we’re aiming to study dozens of wild bee species and broader comparisons are coming. These two studies are really establishing the foundation,” she adds. “The long-term goal is really to be able to use these tools to detect early signatures of stress in wild bees and thereby identify habitats in need of restoration or preservation. We are excited to be building the tools for a new era of wild bee research and conservation.”

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